EMBASSY: CBSTOOLS: elipop

elipop

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

Prediction of lipoproteins

Description

The LipoP 1.0 server produces predictions of lipoproteins and discriminates between lipoprotein signal peptides, other signal peptides and n-terminal membrane helices in Gram negative bacteria.

Usage

Here is a sample session with elipop

% elipop Prediction of lipoproteins Input (aligned) sequence set: 5h2a_crigr.fsa Output file [5h2a_crigr.elipop]:

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

Command line arguments

Prediction of lipoproteins
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.elipop] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -plot               boolean    [N] Produce graphics
   -short              boolean    [N] Short output
   -html               boolean    [N] Html output
   -format             boolean    [N] Run LipoPformat script
   -cutoff             integer    [-3] Log-odds cutoff (Any integer value)

   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

   "-outfile" associated qualifiers
   -odirectory2        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) seqset (Aligned) sequence set filename and optional format, or reference (input USA) Readable set of sequences Required

[-outfile]
(Parameter 2) outfile Output file name Output file <*>.elipop

Additional (Optional) qualifiers

(none)

Advanced (Unprompted) qualifiers

-plot boolean Produce graphics Boolean value Yes/No No

-short boolean Short output Boolean value Yes/No No

-html boolean Html output Boolean value Yes/No No

-format boolean Run LipoPformat script Boolean value Yes/No No

-cutoff integer Log-odds cutoff Any integer value -3

Associated qualifiers

"-sequence" associated seqset 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

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile 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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1)	seqset	(Aligned) sequence set filename and optional format, or reference (input USA)	Readable set of sequences	Required
[-outfile] (Parameter 2)	outfile	Output file name	Output file	<>*.elipop
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-plot	boolean	Produce graphics	Boolean value Yes/No	No
-short	boolean	Short output	Boolean value Yes/No	No
-html	boolean	Html output	Boolean value Yes/No	No
-format	boolean	Run LipoPformat script	Boolean value Yes/No	No
-cutoff	integer	Log-odds cutoff	Any integer value	-3
Associated qualifiers
"-sequence" associated seqset 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
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	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

elipop reads any normal sequence USAs.

Input files for usage example

File: 5h2a_crigr.fsa

>5H2A_CRIGR you can have comments after the ID
MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL
QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP
LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF
GLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFL
PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE
HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA
GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV

Output file format

elipop outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: 5h2a_crigr.elipop

# 5H2A_CRIGR you can have comments after the ID
# len 70
# lett A:2 C:2 D:7 E:4 F:2 G:4 H:1 I:4 K:0 L:8 M:2 N:8 P:3 Q:1 R:3 S:11 T:4 V:1 W:1 Y:2
5H2A_CRIGR	LipoP1.0	SEQUENCE	1	70	0	+	.	#you can have comments after the ID
5H2A_CRIGR	LipoP1.0:Signal	CYT	1	1	-0.200913	+	0	#M

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
antigenic	Finds antigenic sites in proteins
digest	Reports on protein proteolytic enzyme or reagent cleavage sites
echlorop	Reports presence of chloroplast transit peptides
eiprscan	Motif detection
emast	Motif detection
ememe	Multiple EM for Motif Elicitation
ememetext	Multiple EM for Motif Elicitation. Text file only
enetnglyc	Reports N-glycosylation sites in human proteins
enetoglyc	Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
enetphos	Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
epestfind	Finds PEST motifs as potential proteolytic cleavage sites
eprop	Reports propeptide cleavage sites in proteins
esignalp	Reports protein signal cleavage sites
etmhmm	Reports transmembrane helices
eyinoyang	Reports O-(beta)-GlcNAc attachment sites
fuzzpro	Search for patterns in protein sequences
fuzztran	Search for patterns in protein sequences (translated)
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences
oddcomp	Identify proteins with specified sequence word composition
omeme	Motif detection
patmatdb	Searches protein sequences with a sequence motif
patmatmotifs	Scan a protein sequence with motifs from the PROSITE database
pepcoil	Predicts coiled coil regions in protein sequences
preg	Regular expression search of protein sequence(s)
pscan	Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave	Reports on signal cleavage sites in a protein sequence

Author(s)

This program is an EMBOSS wrapper for a program written by the CBS group http://www.cbs.dtu.dk/index.shtml

The original CBS group application must be licensed and installed to use this wrapper.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

File: 5h2a_crigr.fsa

Output file format

Output files for usage example

File: 5h2a_crigr.elipop

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments