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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
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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
(Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | <*>.elipop |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -plot | Produce graphics | Boolean value Yes/No | No |
| -short | Short output | Boolean value Yes/No | No |
| -html | Html output | Boolean value Yes/No | No |
| -format | Run LipoPformat script | Boolean value Yes/No | No |
| -cutoff | Log-odds cutoff | Any integer value | -3 |
>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 |
| digest | Reports on protein proteolytic enzyme or reagent cleavage sites |
| echlorop | Reports presence of chloroplast transit peptides |
| eiprscan | Motif detection |
| emast | Motif detection |
| ememe | Motif detection |
| 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 |
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.