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ebi_tmhmm |
ebi_tmhmm transforms the result sent by the EBI Web server into a file in GFF format, which can easily be given as input to other EMBOSS programs or to any software that supports GFF format. ebi_tmhmm also automatically starts the EMBOSS program showfeat to provide a panoramic overview of the localization of the predicted transmembrane segments. For an input protein sequence it also automatically starts the EMBOSS Embassadir program topo to make a graphical representation.
Note that the EBI sometimes disables nucleic acid searches and in this case a nucleic acid query might yield no result, although there actually are transmembrane coding segments. You can check in the InterProScan home page whether this is currently the case.
TMHMM is based upon a Hidden Markov Model (HMM) architecture. The architecture is made up of 7 types of states corresponding to the core of the transmembrane helix, helix caps, cytoplasmic loops, short and long cytoplasmic loop states, and globular domains that are part of each loop. The prediction of transmembrane helices is done by finding an optimal alignment of the sequence with the model using the N-Best algorithm. In the N-Best algorithm, the algorithm uses the model architecture to find the best labeling of the sequence, given the model.
> ebi_tmhmm Reports membrane spanning regions using EBI Web Services Input sequence: sw:opsd_human Output file [opsd_human.ebi_tmhmm]: Graph type [x11]: cps Starting topo with parameter -sections=39-59,74-96,115-133,154-174,202-222,254-276,286-306 Created topo.ps |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] sequence Sequence filename and optional format, or
reference (input USA)
[-outfile] outfile [*.ebi_tmhmm] Output file name
* -graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
Additional (Optional) qualifiers (* if not always prompted):
* -orfminsize integer [100] Minimum open reading frame size. Open
reading frames of at least this size
(default = 100) are translated and analyzed.
(Integer 0 or more, but not > sequence
length)
* -gencode menu [0] Genetic code for translating sequence
(Values: 0 (Standard); 1 (Standard (with
alternative initiation codons)); 2
(Vertebrate Mitochondrial); 3 (Yeast
Mitochondrial); 4 (Mold, Protozoan,
Coelenterate Mitochondrial and
Mycoplasma/Spiroplasma); 5 (Invertebrate
Mitochondrial); 6 (Ciliate Macronuclear and
Dasycladacean); 9 (Echinoderm
Mitochondrial); 10 (Euplotid Nuclear); 11
(Bacterial); 12 (Alternative Yeast Nuclear);
13 (Ascidian Mitochondrial); 14 (Flatworm
Mitochondrial); 15 (Blepharisma
Macronuclear); 16 (Chlorophycean
Mitochondrial); 21 (Trematode
Mitochondrial); 22 (Scenedesmus obliquus);
23 (Thraustochytrium Mitochondrial))
Advanced (Unprompted) qualifiers:
-[no]showfeat boolean [Y] Call showfeat to show position membrane
spanning regions in sequence
-[no]topo boolean [Y] Open output with topo (only for protein)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the 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
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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) |
Sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||||||||||||||||||||||||||||||
| [-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.ebi_tmhmm | ||||||||||||||||||||||||||||||||||||
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 | ||||||||||||||||||||||||||||||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -orfminsize | Minimum open reading frame size. Open reading frames of at least this size (default = 100) are translated and analyzed. | Integer 0 or more, but not > sequence length | 100 | ||||||||||||||||||||||||||||||||||||
| -gencode | Genetic code for translating sequence |
|
0 | ||||||||||||||||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||||||||||||||||||||||||||||||
| -[no]showfeat | Call showfeat to show position membrane spanning regions in sequence | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
| -[no]topo | Open output with topo (only for protein) | Boolean value Yes/No | Yes | ||||||||||||||||||||||||||||||||||||
OPSD_HUMAN TMHMM transmembrane_regions 39 59 . . . OPSD_HUMAN TMHMM transmembrane_regions 74 96 . . . OPSD_HUMAN TMHMM transmembrane_regions 115 133 . . . OPSD_HUMAN TMHMM transmembrane_regions 154 174 . . . OPSD_HUMAN TMHMM transmembrane_regions 202 222 . . . OPSD_HUMAN TMHMM transmembrane_regions 254 276 . . . OPSD_HUMAN TMHMM transmembrane_regions 286 306 . . . |
OPSD_HUMAN
Rhodopsin (Opsin-2).
|==========================================================| 348
|---| |---| |--| |---| |---| |---| |--| transmembrane_regions
|
![[topo result]](ebi_tmhmm_topo.png)
None.
You can give the GFF file written by ebi_tmhmm as input to other EMBOSS
programs by composing a command line of type :
<program> <sequence> -ufo=<GFF file>
The length of the sequence is longer than the maximum of 5000 allowed for nucleic acid sequences
It can happen that the submission of the job fails or that anyhow the job ID number has not been successfully retrieved and stored. In that case ebi_tmhmm will give up and issue the message :
ERROR !! EBI Web Server failed to return job ID
There are various error messages related to the retrieval of the result of a submitted job :
EBI Web Server failed to respond on <date+time> you can later try manual check with command : /opt/sw/EBIWS/interproscan.pl --status --jobid <jobid>
ERROR !! some error occurred on the EBI Web Server
ERROR !! EBI Web Server could not retrieve job result
ERROR !! EBI Web Server executed job but failed to retrieve output
job still not finished after more than 30 h. I QUIT. you can try manual check with command : /opt/sw/EBIWS/interproscan.pl --status --jobid <jobid>
It can happen that the algorithm fails to find likely potential transmembrane segments in the sequence. In that case you will get the message :
No transmembrane regions were found !
| Program name | Description |
|---|---|
| garnier | Predicts protein secondary structure |
| helixturnhelix | Report nucleic acid binding motifs |
| hmoment | Hydrophobic moment calculation |
| jpred | Predicts protein secondary structure using neural networks |
| pepcoil | Predicts coiled coil regions |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| proftmb | Reports transmembrane beta barrels |
| tmap | Displays membrane spanning regions |
| topo | Draws an image of a transmembrane protein |
| ebi_blast | WU-BLAST search of query sequence against sequence databank using EBI Web Services |
| ebi_fasta | fastA search of query sequence against sequence databank using EBI Web Services |
The program TMHMM itself was written by A. Krogh, E. L. L. Sonnhammer and G. von Heijne, Center for Biological Sequence Analysis, Technical University of Denmark. The SOAP based Web services client and server were developed at the EMBL-EBI (Hinxton, UK).