elipop |
Please help by correcting and extending the Wiki pages.
% elipop Prediction of 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
Prediction of lipoproteins Version: EMBOSS:6.4.0.0 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 -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) 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 |
-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 |
>5H2A_CRIGR you can have comments after the ID MEILCEDNTSLSSIPNSLMQVDGDSGLYRNDFNSRDANSSDASNWTIDGENRTNLSFEGYLPPTCLSILHL QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP LPSKLCAVWIYLDVLFSTASIMHLCAISLDRYVAIQNPIHHSRFNSRTKAFLKIIAVWTISVGVSMPIPVF GLQDDSKVFKQGSCLLADDNFVLIGSFVAFFIPLTIMVITYFLTIKSLQKEATLCVSDLSTRAKLASFSFL PQSSLSSEKLFQRSIHREPGSYTGRRTMQSISNEQKACKVLGIVFFLFVVMWCPFFITNIMAVICKESCNE HVIGALLNVFVWIGYLSSAVNPLVYTLFNKTYRSAFSRYIQCQYKENRKPLQLILVNTIPALAYKSSQLQA GQNKDSKEDAEPTDNDCSMVTLGKQQSEETCTDNINTVNEKVSCV |
# 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 |
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
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 |
epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
esignalp | Reports 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 | Searches 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 | Scans protein sequence(s) with fingerprints from the PRINTS database |
sigcleave | Reports on signal cleavage sites in a protein sequence |
siggenlig | Generates ligand-binding signatures from a CON file |
sigscan | Generates hits (DHF file) from a signature search |
tmap | Predict and plot transmembrane segments in protein sequences |
topo | Draws an image of a transmembrane protein |
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.