seqret

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Function

Description

seqret reads in one or more sequences and writes them out again. The sequence input may be a literal sequence or read from a database, file, file of sequence names, or even the command-line or the output of another programs. The sequence output can be written to screen, to file, or passed to another program. A wide range of standard sequence formats may be specified for input and output. If you don't specify the input format, seqret will try a set of possible formats until it reads it in successfully. The sequence input and output, as for all EMBOSS programs, is described by a Uniform Sequence Address. This is is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.

There are many options built-in into EMBOSS for detailed specification of the input and output sequences, for example the sequence type, file format. specification of sequence regions by begin and end positions, or generation of the reverse complement of a nucleic acid sequence. On output seqret can change the case of the sequence to upper or to lower case.

seqret is useful for a variety of tasks, including extracting sequences from databases, displaying sequences, reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.

Usage

Extract an entry from a database and write it to a file:

% seqret Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]:

Go to the input files for this example
Go to the output files for this example

Example 2

Read all entries in the database 'tembl' that start with 'ab' and write them to a file. In this example the specification is all done in the command line and to stop Unix getting confused by the '*' character, it has to have a backslash ('\') before it:

% seqret 'tembl:ab*' aball.seq Reads and writes (returns) sequences

Go to the output files for this example

Example 3

seqret does not read in features by default because this results in slightly faster performance. If however you wish to read in features with your sequence and write them out on output, using '-feature' will change the default behaviour to use any features present in the sequence. N.B. use embl format for the output file as the default format 'fasta' reports the features in gff (file "<seqname>.gff")

% seqret -feature Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: embl::x65923.embl

Go to the output files for this example

Example 4

Display the contents of the sequence on the screen:

% seqret Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: stdout >X65923 X65923.1 H.sapiens fau mRNA ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttcagtcaaaaaaaaaa

Example 5

Write the result in GCG format by using the qualifier '-osformat'.

% seqret -osf gcg Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.gcg]:

Go to the output files for this example

Example 6

Write the result in GCG format by specifying the format in the output USA on the command line.

% seqret -outseq gcg::x65923.gcg Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923

Example 7

Write the result in GCG format by specifying the format in the output USA at the prompt.

% seqret Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]: gcg::x65923.gcg

Example 8

Write the reverse-complement of a sequence:

% seqret -srev Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]:

Go to the output files for this example

Example 9

Extract the bases between the positions starting at 5 and ending at 25:

% seqret -sbegin 5 -send 25 Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]:

Go to the output files for this example

Example 10

Extract the bases between the positions starting at 5 and ending at 5 bases before the end of the sequence:

% seqret -sbegin 5 -send -5 Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:x65923 output sequence(s) [x65923.fasta]:

Go to the output files for this example

Example 11

Read all entries in the database 'tembl' that start with 'h' and write them to a file:

% seqret Reads and writes (returns) sequences Input (gapped) sequence(s): tembl:h* output sequence(s) [h45989.fasta]: hall.seq

Go to the output files for this example

Command line arguments

Reads and writes (returns) sequences
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -feature            boolean    Use feature information
   -firstonly          boolean    [N] Read one sequence and stop

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1)	seqall	(Gapped) sequence(s) filename and optional format, or reference (input USA)	Readable sequence(s)	Required
[-outseq] (Parameter 2)	seqoutall	Sequence set(s) filename and optional format (output USA)	Writeable sequence(s)	<*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-feature	boolean	Use feature information	Boolean value Yes/No	No
-firstonly	boolean	Read one sequence and stop	Boolean value Yes/No	No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence	integer	Start of each sequence to be used	Any integer value	0
-send1 -send_sequence	integer	End of each sequence to be used	Any integer value	0
-sreverse1 -sreverse_sequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_sequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_sequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_sequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_sequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_sequence	boolean	Make upper case	Boolean value Yes/No	N
-sformat1 -sformat_sequence	string	Input sequence format	Any string
-sdbname1 -sdbname_sequence	string	Database name	Any string
-sid1 -sid_sequence	string	Entryname	Any string
-ufo1 -ufo_sequence	string	UFO features	Any string
-fformat1 -fformat_sequence	string	Features format	Any string
-fopenfile1 -fopenfile_sequence	string	Features file name	Any string
"-outseq" associated seqoutall qualifiers
-osformat2 -osformat_outseq	string	Output seq format	Any string
-osextension2 -osextension_outseq	string	File name extension	Any string
-osname2 -osname_outseq	string	Base file name	Any string
-osdirectory2 -osdirectory_outseq	string	Output directory	Any string
-osdbname2 -osdbname_outseq	string	Database name to add	Any string
-ossingle2 -ossingle_outseq	boolean	Separate file for each entry	Boolean value Yes/No	N
-oufo2 -oufo_outseq	string	UFO features	Any string
-offormat2 -offormat_outseq	string	Features format	Any string
-ofname2 -ofname_outseq	string	Features file name	Any string
-ofdirectory2 -ofdirectory_outseq	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

Input files for usage example

Database entry: tembl:x65923

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   H-InvDB; HIT000322806.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

Output file format

If the '-firstonly' qualifier is used then only the first sequence of the input USA specification will be written out.

In some cases the output filename will be the same as the input filename, but as seqret reads only the first sequence before opening the output file it may try to overwrite the input. Note that this is not true of seqretset which reads all sequences into memory at startup, but which can need a large amount of memory for many sequences.

Output files for usage example

File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

Output files for usage example 2

File: aball.seq

>AB009602 AB009602.1 Schizosaccharomyces pombe mRNA for MET1 homolog, partial cds.
gttcgatgcctaaaataccttcttttgtccctacacagaccacagttttcctaatggctt
tacaccgactagaaattcttgtgcaagcactaattgaaagcggttggcctagagtgttac
cggtttgtatagctgagcgcgtctcttgccctgatcaaaggttcattttctctactttgg
aagacgttgtggaagaatacaacaagtacgagtctctcccccctggtttgctgattactg
gatacagttgtaatacccttcgcaacaccgcgtaactatctatatgaattattttccctt
tattatatgtagtaggttcgtctttaatcttcctttagcaagtcttttactgttttcgac
ctcaatgttcatgttcttaggttgttttggataatatgcggtcagtttaatcttcgttgt
ttcttcttaaaatatttattcatggtttaatttttggtttgtacttgttcaggggccagt
tcattatttactctgtttgtatacagcagttcttttatttttagtatgattttaatttaa
aacaattctaatggtcaaaaa
>AB000095 AB000095.1 Homo sapiens mRNA for hepatocyte growth factor activator inhibitor, complete cds.
cggccgagcccagctctccgagcaccgggtcggaagccgcgacccgagccgcgcaggaag
ctgggaccggaacctcggcggacccggccccacccaactcacctgcgcaggtcaccagca
ccctcggaacccagaggcccgcgctctgaaggtgacccccctggggaggaaggcgatggc
ccctgcgaggacgatggcccgcgcccgcctcgccccggccggcatccctgccgtcgcctt
gtggcttctgtgcacgctcggcctccagggcacccaggccgggccaccgcccgcgccccc
tgggctgcccgcgggagccgactgcctgaacagctttaccgccggggtgcctggcttcgt
gctggacaccaacgcctcggtcagcaacggagctaccttcctggagtcccccaccgtgcg
ccggggctgggactgcgtgcgcgcctgctgcaccacccagaactgcaacttggcgctagt
ggagctgcagcccgaccgcggggaggacgccatcgccgcctgcttcctcatcaactgcct
ctacgagcagaacttcgtgtgcaagttcgcgcccagggagggcttcatcaactacctcac
gagggaagtgtaccgctcctaccgccagctgcggacccagggctttggagggtctgggat
ccccaaggcctgggcaggcatagacttgaaggtacaaccccaggaacccctggtgctgaa
ggatgtggaaaacacagattggcgcctactgcggggtgacacggatgtcagggtagagag
gaaagacccaaaccaggtggaactgtggggactcaaggaaggcacctacctgttccagct
gacagtgactagctcagaccacccagaggacacggccaacgtcacagtcactgtgctgtc
caccaagcagacagaagactactgcctcgcatccaacaaggtgggtcgctgccggggctc
tttcccacgctggtactatgaccccacggagcagatctgcaagagtttcgtttatggagg
ctgcttgggcaacaagaacaactaccttcgggaagaagagtgcattctagcctgtcgggg
tgtgcaaggcccctccatggaaaggcgccatccagtgtgctctggcacctgtcagcccac
ccagttccgctgcagcaatggctgctgcatcgacagtttcctggagtgtgacgacacccc
caactgccccgacgcctccgacgaggctgcctgtgaaaaatacacgagtggctttgacga
gctccagcgcatccatttccccagtgacaaagggcactgcgtggacctgccagacacagg
actctgcaaggagagcatcccgcgctggtactacaaccccttcagcgaacactgcgcccg
ctttacctatggtggttgttatggcaacaagaacaactttgaggaagagcagcagtgcct
cgagtcttgtcgcggcatctccaagaaggatgtgtttggcctgaggcgggaaatccccat
tcccagcacaggctctgtggagatggctgtcgcagtgttcctggtcatctgcattgtggt
ggtggtagccatcttgggttactgcttcttcaagaaccagagaaaggacttccacggaca
ccaccaccacccaccacccacccctgccagctccactgtctccactaccgaggacacgga
gcacctggtctataaccacaccacccggcccctctgagcctgggtctcaccggctctcac
ctggccctgcttcctgcttgccaaggcagaggcctgggctgggaaaaactttggaaccag
actcttgcctgtttcccaggcccactgtgcctcagagaccagggctccagcccctcttgg
agaagtctcagctaagctcacgtcctgagaaagctcaaaggtttggaaggagcagaaaac
ccttgggccagaagtaccagactagatggacctgcctgcataggagtttggaggaagttg
gagttttgtttcctctgttcaaagctgcctgtccctaccccatggtgctaggaagaggag
tggggtggtgtcagaccctggaggccccaaccctgtcctcccgagctcctcttccatgct
gtgcgcccagggctgggaggaaggacttccctgtgtagtttgtgctgtaaagagttgctt
tttgtttatttaatgctgtggcatgggtgaagaggaggggaagaggcctgtttggcctct
ctgtcctctcttcctcttcccccaagattgagctctctgcccttgatcagccccaccctg


  [Part of this file has been deleted for brevity]

nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnntcctgtcctcccgtccatcctctgttcccgggttctcctgcccctttccct
ccccttcctcctcctccatggcctcttcgcctgcccatgctctgtgtgtattgcaggttt
cccagttcatggcgtgtgaggagctgcccccgggggccccagagcttccccaagaaggcc
ccacacgacgcctctccctaccgggccagctgggggccctcacctcccagcccctgcaca
gacacggctcggacccgggcagttagtggggctgcccagtgtggacacgt
>AB000360 AB000360.1 Homo sapiens PIGC gene, complete cds.
ggatccctgctgcagagggggtaacggtgtctggcttgccaagcaatatttgttgtggtc
tatcatggaagaaataaagtcgggcaatatgaattttttttttctcaaatttgccggatg
gctgtggtgtttctgactcttagttttctcattgtgaaaaaggaatgattatcttcttcg
atcctctcaagagtttccttgttttgagtagattgatagctctttaaaggatgctaagct
cagctaatggaagaagagtctagtttctttgaggctttgattttggttaaactatagagc
tcatacctttctgtatggtgcagcttactattgtctttggattggtaacttaaaaaatac
aaataacatgcctttgagaaccaataaaaactatggatattatccctataaatttacaca
aatccagatataagcatgcaatgtgatatacctaagggatatgtgaaccactgagttaag
aactgctttagagggagatacaatgtgagacacaggctttgggataagactttggtttga
atcctggctctgctctgttaccttagggcaaagttacttaagcatcttgaatctcagctt
ttttaccaaagcaggactaatactaacttacaaggtggtgaggattaagtgaaagaagat
acataaggcacttagcacatagtaggtactcaataagcgatagctaacagatgtctatta
ttattcaaggaattataattttcaaatctgaaatgcagttttaatgtcccataaggtgac
taccacatacatttttctcagacttttagtaaactgagttgatttgactttatctcagta
ctactcttgacctttcacaactttcgtaggttcacagtctctctttttctaggaacttgg
ctgtgttgtcctgcctcagagacaaattcatctattgtaggcctagcccctgcctttgaa
aacaaggaaaggttggtagaacatcaacacagcatggaatttccagggaggtctcatttc
aaaacttcataaagaacaagaaccacctggacttctgtgagggcgatgattaaactggcc
tgagtttgaatgaaaggataatgtatgctcaacctgtgactaacaccaaggaggtcaagt
ggcagaaggtcttgtatgagcgacagccctttcctgataactatgtggaccggcgattcc
tggaagagctccggaaaaacatccatgctcggaaataccaatattgggctgtggtatttg
agtccagtgtggtgatccagcagctgtgcagtgtttgtgtttttgtggttatctggtggt
atatggatgagggtcttctggccccccattggcttttagggactggcctggcttcttcac
tgattgggtatgttttgtttgatctcattgatggaggtgaagggcggaagaagagtgggc
agacccggtgggctgacctgaagagtgccctagtcttcattactttcacttatgggtttt
caccagtgctgaagacccttacagagtctgtcagcactgacaccatctatgccatgtcag
tcttcatgctgttaggccatctcatcttttttgactatggtgccaatgctgccattgtat
ccagcacactatccttgaacatggccatctttgcttctgtatgcttggcatcacgtcttc
cccggtccctgcatgccttcatcatggtgacatttgccattcagatttttgccctgtggc
ccatgttgcagaagaaactaaaggcatgtactccccggagctatgtgggggtcacactgc
tttttgcattttcagccgtgggaggcctactgtccattagtgctgtgggagccgtactct
ttgcccttctgctgatgtctatctcatgtctgtgttcattctacctcattcgcttgcagc
tttttaaagaaaacattcatgggccttgggatgaagctgaaatcaaggaagacttgtcca
ggttcctcagttaaattaggacatccattacattattaaagcaagctgatagattagcct
cctaactagtatagaacttaaagacagagttccattctggaagcagcatgtcattgtggt
aagagaatagagatcaaaaccaaaaaaaatgaaccaaaggcttgggtggtgagggtgctt
atcctttctgttattttgtagatgaaaaaactttctggggacctcttgaattacatgctg
taacatatgaagtgatgtggtttctattaaaaaaataacacatccatcaagttgtctcat
gatttttccataaacaggaggcagacagaggggcatgaagagtgaagtaagtgtgtgtgt
gtgtgtgtgtgtgtgtaaagtcacttctttctacccttttcaatgtgctaatgctctttt
atttatctagggctcaaatcttagaacacagggtgctatgctcagttttgttgcccaaga
tcacagaattggttacttaaccttgactcagagtttctaccttgttcttagggaagcata
tcacaactaattgcaaagcagagtgtgatgtgtcacaataagcagaatgctagggggaat
tc

Output files for usage example 3

File: x65923.embl

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM.
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   H-InvDB; HIT000322806.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

Output files for usage example 5

File: x65923.gcg

!!NA_SEQUENCE 1.0

H.sapiens fau mRNA

X65923  Length: 518  Type: N  Check: 2981 ..

   1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc

  51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt

 101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg

 151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg

 201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct

 251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc

 301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag

 351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg

 401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca

 451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta

 501 gttcagtcaa aaaaaaaa

Output files for usage example 8

File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
ttttttttttgactgaactaagtggcttttttattagagaaagccagaattacaaaagac
ttaagagttggcattggggcccttcttcttgccaaaggtgggcacaacgttgacaaagcg
ccggttgtactgcatccgccgcttagcccgacctgtcttcttcttcttcttctcctgttt
ggccaccttaggagtctgacctctcacttttccagcacgggccagggaaccatgaacttt
acctccaagcatgcggcctgctacttccagggtagtcagggcctccaccccgcactggcc
cagagtggcctcatcctccaggggcgcgcctgccaggagcacgacttgatcttccggggc
aatgccctccagtgaggctacatgagccttgatctgggcgaccgtttcctggccggtcac
ctcgaaggtgtgtagctcctgggcgcggacaaagagctgcatattggcgactgaacggcg
gtcccagctaccgcgaagatggagtcgagaaagaggaa

Output files for usage example 9

File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcg

Output files for usage example 10

File: x65923.fasta

>X65923 X65923.1 H.sapiens fau mRNA
tctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagct
ctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgccca
gatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcct
ggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgac
taccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgc
tggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagac
aggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccacctt
tggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctcta
ataaaaaagccacttagttcagtcaaaaaa

Output files for usage example 11

File: hall.seq

>H45989 H45989.1 yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone IMAGE:177794 3', mRNA sequence.
ccggnaagctcancttggaccaccgactctcgantgnntcgccgcgggagccggntggan
aacctgagcgggactggnagaaggagcagagggaggcagcacccggcgtgacggnagtgt
gtggggcactcaggccttccgcagtgtcatctgccacacggaaggcacggccacgggcag
gggggtctatgatcttctgcatgcccagctggcatggccccacgtagagtggnntggcgt
ctcggtgctggtcagcgacacgttgtcctggctgggcaggtccagctcccggaggacctg
gggcttcagcttcccgtagcgctggctgcagtgacggatgctcttgcgctgccatttctg
ggtgctgtcactgtccttgctcactccaaaccagttcggcggtccccctgcggatggtct
gtgttgatggacgtttgggctttgcagcaccggccgccgagttcatggtngggtnaagag
atttgggttttttcn

Data files

Notes

seqret is often one of the first programs taught in EMBOSS training courses. This is because it is versatile, it is extremely powerful for its size (17 lines of code) it illustrates many aspects of EMBOSS programs and it was one of the first EMBOSS programs to be written, so it has a special place in the hearts of EMBOSS developers.

The name 'seqret' derives both from its function ("sequence return") and from the fact that immense amounts of functionality can come from so few lines of source code - most of the work is done by the EMBOSS libraries which the program calls and whose complexity is hidden, or "secret".

The simplicity of the above description of this program greatly understates the rich functionality of this program.

Because EMBOSS programs can take a wide range of qualifiers that slightly change the behaviour of the program when reading or writing a sequence, this program can do many more things than simply "read and write a sequence".

seqret can read a sequence or many sequences from databases, files, files of sequence names, the command-line or the output of other programs and then can write them to files, the screen or pass them to other programs. Because it can read in a sequence from a database and write it to a file, seqret is a program for extracting sequences from databases. Because it can write the sequence to the screen, seqret is a program for displaying sequences.

seqret can read sequences in any of a wide range of standard sequence formats. You can specify the input and output formats being used. If you don't specify the input format, seqret will try a set of possible formats until it reads it in successfully. Because you can specify the output sequence format, seqret is a program to reformat a sequence.

seqret can read in the reverse complement of a nucleic acid sequence. It therefore is a program for producing the reverse complement of a sequence.

seqret can read in a sequence whose begin and end positions you have specified and write out that fragment. It is therefore a utility for doing simple extraction of a region of a sequence.

seqret can change the case of the sequence being read in to upper or to lower case. It is therefore a simple sequence beautification utility.

seqret can do any combination of the above functions.

The sequence input and output specification of this (and many other EMBOSS programs) is described as being a Uniform Sequence Address.

The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek reference to a URL-style sequence naming used by all EMBOSS applications.

The USA is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications.

See the full specification of USA syntax at:
http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html

The basic USA syntax is one of:

• "file"
• "file:entry"
• "format::file"
• "format::file:entry"
• "database:entry"
• "database"
• "@file"

Note that ':' separates the name of a file containing many possible entries from the specific name of a sequence entry in that file. It also separates the name of a database from an entry in that database

Note also that '::' separates the specified format of a file from the name of the file. Normally the format can be omitted, in which case the program will attempt to identify the correct format when reading the sequence in and will default to using FASTA format when writing the sequence out.

Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'.

Database queries, and individual entries in files that have more than one sequence entry, use wildcards of "?" for any character and "*" for any string of characters. There are some problems with the Unix shell catching these characters so they do need to be hidden in quotes or preceded by a backslash on the Unix command line, (for example "embl:hs\*")

The output USA name 'stdout' is special. It makes the output go to the device 'standard output'. This is the screen, by default.

Example USAs

USA	Description
xxx.seq	A sequence file "xxx.seq" in any format
fasta::xxx.seq	A sequence file "xxx.seq" in fasta format
gcg::egmsmg.gcg	A sequence file "egmsmg.gcg" in GCG 9 format
egmsmg.gcg -sformat=gcg	A sequence file "egmsmg.gcg" in GCG 9 format
embl::x13776.em	A sequence file "x13776.em" in EMBL format
embl:x13776	EMBL entry X13776, using whatever access method is defined locally for the EMBL database
embl:K01793	EMBL entry K01793, using whatever access method is defined locally for the EMBL database and searching by accession number and entry name (K01793 is a secondary accession number in this case for entry J01636)
embl-acc:K01793	EMBL entry X13776, using whatever access method is defined locally for the EMBL database and searching by accession number only
embl-id:x13776	EMBL entry x13776, using whatever access method is defined locally for the EMBL database, and searching by ID only
embl:v0029*	EMBL entries V00290, V00291, and so on, usually in alphabetical order, using whatever access method is defined locally for the EMBL database
embl or EMBL:*	All sequences in the EMBL database
@mylist	Reads file mylist and uses each line as a separate USA. This is standard VMS list file syntax, also used in SRS 4.0 but missing in SRS 5.0 onwards. The list file is a list of USAs (one per line). List files can contain references to other lists files or any other standard USA.
list::mylist	Same as "@mylist" above
'getz -e [embl-id:x13776] |'	The pipe character "|" causes EMBOSS to fire up getz (SRS) to extract entry x13776 from EMBL in EMBL format. Any application or script which writes one or more sequences to stdout can be used in this way.
asis::atacgcagttatctgaccat	So far the shortest USA we could invent. In 'asis' format the name is the sequence so no file needs to be opened. This is a special case. It was intended as a joke, but has proved quite useful for generating command lines when testing.

Input sequence formats

By default, (i.e. if no format is explicitly specified) EMBOSS tries each format in turn until one succeeds.

Input Format	Comments
gcg	GCG 9.x and 10.x format with the format and sequence type identified on the first line of the file
gcg8	GCG 8.x format where anything up to the first line containing ".." is considered as heading, and the remainder is sequence data. This format is complicated by the header appearing to be in other formats such as EMBL, and by the possibility of reading a large amount of data in the wrong format before discovering that there is no ".." line because it is not GCG format after all.
embl em	EMBL entry format, or at least a minimal subset of the fields. The Staden package and others use EMBL or similar formats for sequence data.
swiss sw	SWISSPROT entry format, or at least a minimal subset of the fields.
fasta pearson	FASTA format with an optional accession number after the sequence identifier, eg: >name description or >name accession description and with an optional database name in GCG style fasta format included as part of the sequence identifier, eg: >database:name accession description
ncbi	FASTA format with optional accession number and database name in NCBI style included as part of the sequence identifier. eg >database|accession|id description (and other variants on this theme!)
genbank gb	GENBANK entry format, or at least a minimal subset of the fields.
nbrf pir	NBRF (PIR) format, as used in the PIR database sequence files.
codata	CODATA format.
strider	DNA strider format
clustal aln	ClustalW ALN (multiple alignment) format.
phylip	PHYLIP interleaved multiple alignment format.
acedb	ACeDB format
msf	Wisconsin Package GCG's MSF multiple sequence format.
hennig86	Hennig86 format
jackknifer	Jackknifer format
jackknifernon	Jackknifernon format
nexus paup	Nexus/PAUP format
nexusnon paupnon	Nexusnon/PAUPnon format
treecon	Treecon format
mega	Mega format
meganon	Meganon format
ig	IntelliGenetics format.
staden experiment	The experiment file format used by the "gap" program in the Staden package, where the sequence identifier is optional and the remainer is plain text. Some alternative nucleotide ambiguity codes are used and must be converted.
unknown text plain	Plain text. This is the format with no format. The whole of the file is read in as a sequence. No attempt is made to parse the file contents in any way. Anything is acceptable in this format.
raw	Like unknown/text/plain format except that it accepts only alphanumeric and whitespace characters and rejects anything else.
asis	This is not so much a sequence format as a quick way of entering a sequence on the command line, but it is included here for completeness. Where a filename would normally be given, in asis format there is the sequence itself. An example would be: asis::atacgcagttatctgaccat In 'asis' format the name is the sequence so no file needs to be opened. This is a special case. It was intended as a joke, but could be quite useful for generating command lines.

Output sequence formats

Some sequence formats can hold multiple sequences in one file, these are marked as multiple in the following table. The details of how many sequences are held in one file differs between formats, but they either allow many sequences to be concatenated one after the other, or they hold the sequences together in some sort of aligned set of sequences.

Other formats, such as GCG, plain and staden formats can only hold one sequence per file, these are marked as single. An attempt to concatenate several sequences in one file leaves the results as a mess that makes it impossible to decide where the sequences start and end or what is annotation and what is sequence.

These single formats therefore cause problems when there are multiple sequences to write out because a single file containing multiple sequences in that format is invalid. When these formats are specified for output, an EMBOSS program will allow you to write many sequences to one file, but EMBOSS programs will not be able to reliably read in the resulting mess.

N.B This behaviour changed in EMBOSS version 1.7.0. (31 Oct 2000) Previously, EMBOSS programs that were asked to write multiple sequences in a single format would ignore the requested output file name and would write each sequence into a separate file whose name was constructed from the sequence name and the name of the format. This resulted in ouput to files whose names could not be reliably controlled. A decision was taken that EMBOSS users were intelligent people who could live with the consequences of their actions and who could learn not to write out multiple sequences to a file in formats that could not cope with multiple sequences.

It you really wish to write multiple sequences out in formats that can not cope with multiple sequences, you are advised to add the global qualifier -ossingle on the command line. This will force the EMBOSS program to ignore the given output file name and will generate its own file names. One sequence will be written to each such file. These file names are made from the sequence ID name, with the name of the format as the extension (e.g. x65923.gcg).

This is not ideal. Preferably, you should stay away from formats that can't cope with multiple sequences in a file.

Output Format	Single/ Multiple	Comments
gcg	single	Wisconsin Package GCG 9.x and 10.x format with the sequence type on the first line of the file.
gcg8	single	GCG 8.x format where anything up to the first line containing ".." is considered as heading, and the remainder is sequence data.
embl em	multiple	EMBL entry format with available fields filled in and others with no infomation omitted. The EMBOSS command line allows missing data such as accession numbers to be provided if they are not obtainable from the input sequence.
swiss sw	multiple	SwisProt entry format with available fields filled in and others with no infomation omitted. The EMBOSS command line allows missing data such as accession numbers to be provided if they are not obtainable from the input sequence.
fasta	multiple	Standard Pearson FASTA format, but with the accession number included after the identifier if available.
pearson	multiple	Simple Pearson FASTA format, an alias for "fasta" format.
ncbi	multiple	NCBI style FASTA format with the database name, entry name and accession number separated by pipe ("|") characters.
nbrf pir	multiple	NBRF (PIR) format, as used in the PIR database sequence files.
genbank gb	multiple	GENBANK entry format with available fields filled in and others with no infomation omitted. The EMBOSS command line allows missing data such as accession numbers to be provided if they are not obtainable from the input sequence.
ig	multiple	Intelligenetics format, as used by the Intelligenetics package
codata	multiple	CODATA format.
strider	multiple	DNA strider format
acedb	multiple	ACeDB format
staden experiment	single	The experiment file format used by the "gap" program in the Staden package. Some alternative nucleotide ambiguity codes are used and are converted.
text plain raw	single	Plain sequence, no annotation or heading.
fitch	multiple	Fitch format
msf	multiple	Wisconsin Package GCG's MSF multiple sequence format.
clustal aln	multiple	Clustal multiple sequence format.
phylip	multiple	PHYLIP non-interleaved format.
phylip3	multiple	PHYLIP interleaved format.
asn1	multiple	A subset of ASN.1 containing entry name, accession number, description and sequence, similar to the current ASN.1 output of readseq
hennig86	multiple	Hennig86 format
mega	multiple	Mega format
meganon	multiple	Meganon format
nexus paup	multiple	Nexus/PAUP format
nexusnon paupnon	multiple	Nexusnon/PAUPnon format
jackknifer	multiple	Jackknifer format
jackknifernon	multiple	Jackknifernon format
treecon	multiple	Treecon format
debug	multiple	EMBOSS sequence object report for debugging showing all available fields. Not all fields will contain data - this depends very much on the input format used.

Future directions

Associated qualifiers

As noted previously there are many 'associated' qualifiers that alter the behaviour of seqret when it reads in or writes out a sequence. As these are used in all EMBOSS programs that read in or write out sequences, they are not reported by the '-help' qualifier. They are however reported by the pair of qualifiers: '-help -verbose':

Some of the more useful associated qualifiers are:

Qualifier	Description
-sbegin	The first position to be used in the sequence
-send	The last position to be used in the sequence
-sreverse	Use the reverse complement of a nucleic acid sequence
-sask	Ask the user for begin/end/reverse information
-slower	Convert the sequence to lower case
-supper	Convert the sequence to upper case
-sformat	Specify the input sequence format
-osformat	Specify the output sequence format
-ossingle	Write each entry into a separate file
-auto	Turn off prompts and don't report the one-line description
-stdout	Write the results to 'standard output' (the screen)
-filter	Read input from another program, write to the screen
-options	Prompt for optional qualifiers
-help	Display a table of the command-line options

The set of associated qualifiers for sequences behave in different ways depending on where they appear.

If these qualifiers immediately follow a parameter they apply only to that parameter and not to all cases. If they occur before any parameters, they apply to all following sequence parameters.

If there are no two parameters of equal type, the order of parameters and their qualifiers is irrelevant.

Where a qualifier is defined more than once, for example "-sformat" for 2 input sequences to be aligned, the qualifier name can have a number to indicate which sequence is meant. "-sbegin2=25" will apply only to the second sequence, no matter where it appears on the command line.

The -sbegin and -send qualifiers take an integer number specifying the position to begin or end reading a sequence. If the number is positive, the number is the position counting from the first base or residue of the sequence. If the number is negative the position is counted from the end of the sequence, so position -1 is the last base or residue of the sequence. (If -sbegin 0 is used, it is assumed to be the same as -sbegin 1 and -send 0 is the same as -send -1.)

The filter qualifier makes the program behave like a filter, reading its (first) input 'file' from the standard input, and writing its (first) output 'file' to the standard output. The -filter qualifier will also invoke the -auto qualifier, so the user is never prompted for any missing values.

Example:

% cat sequence.seq | seqret -filter | lpr

The example shows the application seqret being run with the -filter qualifier. The input file is 'piped' into the program using the unix command cat and the output is 'piped' directly to the unix program lpr, which will print it on the printer.

When the -options qualifier is used and not all the parameters are given on the command line, it will query the user for those parameters. It will not only query the user for the required parameters as it would do without the -options qualifier, but it will also query the user for the optional parameters.

When the -stdout qualifier is used, the user will still be prompted for all the info that is required, but will write to standard output by default. The user will also still be prompted for an output filename, in case the user wants to save the output to a file.

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'.

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

Comments

Fasta output format

Question

>AF102796 AF102796 Homo sapiens alphaE-catenin (CTNNA1) gene, exon 11.

Answer

There are many "FASTA formats". EMBOSS uses the format that ACEDB and the EBI genome projects use. The first field after the ID is the accession number, so that accession numbers can be kept when sequences are converted to FASTA format, without using the NCBI format (with '|' characters in the IDs).

Your EMBL format file has IDs that look like accession numbers, so EMBOSS fills in the accession number for each sequence, and reports it in the FASTA format.