                                   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


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 (c) 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
