elipop

 

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Function

Predict 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 
Predict lipoproteins
Input (aligned) protein 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 

Predict lipoproteins
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) protein 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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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) protein 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
-scircular1
-scircular_sequence		 boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence		 boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-iquery1
-iquery_sequence		 string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence		 integer Input start position offset Any integer value 0
-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.

See also

Program name Description
antigenic Find antigenic sites in proteins
echlorop Report 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
epestfind Find PEST motifs as potential proteolytic cleavage sites
esignalp Report protein signal cleavage sites
etmhmm Reports transmembrane helices
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
omeme Motif detection
patmatdb Search protein sequences with a sequence motif
patmatmotifs Scan a protein sequence with motifs from the PROSITE database
preg Regular expression search of protein sequence(s)
pscan Scan protein sequence(s) with fingerprints from the PRINTS database
sigcleave Report on signal cleavage sites in a protein sequence
siggenlig Generate ligand-binding signatures from a CON file
sigscan Generate hits (DHF file) from a signature search
tmap Predict and plot transmembrane segments in protein sequences
topo Draw an image of a transmembrane protein

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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) 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