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kglimmer |
Function
Finding gene in prokaryotic genomes using glimmerDescription
kglimmer finds genes in prokaryotic genomes utilizing Glimmer (Gene Locator and Interpolated Markov Modeler). Glimmer identifies coding regions from given DNA sequence using Interpolated Markov Models (IMM).kglimmer utilizes GLIMMER web service provided by NCBI (National Center for Biotechnology Information). Therefore, users can use kglimmer without preparing their own training data set. Original web-service is located at the following URL:
http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi
This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kglimmer is thus an interface of "runGlimmer" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://soap.g-language.org/kbws/ for more information.
Usage
Here is a sample session with kglimmer % kglimmer Finding genes in prokaryotic genomes using glimmer Input (gapped) sequence(s): refseq:NC_000908 output sequence(s) [nc_000908.kglimmer]: Jobid: kbws_5626576 ************** GLIMMER (ver. 3.02; iterated) predictions: orfID start end frame score -------- ----- ----- -- ----- >NC_000908 orf00001 579846 3 +1 3.70 orf00002 686 1828 +2 5.73 orf00003 1828 2073 +1 9.65 orf00005 2605 2760 +1 1.81 orf00006 2845 2979 +1 5.92 orf00007 3010 3255 +1 6.99 orf00009 3319 3513 +1 7.25 orf00010 3529 4557 +1 9.81 orf00012 4645 4797 +1 14.04 orf00014 4812 7322 +3 7.39 orf00015 7294 7857 +1 9.49 orf00016 8107 8295 +1 8.36 orf00018 8296 8547 +1 11.93 orf00020 8551 9183 +1 10.33 orf00021 9156 9323 +3 3.04 orf00022 9468 9755 +3 9.01 orf00023 9923 11059 +2 10.73 orf00024 11251 11892 +1 9.46 orf00025 12068 12244 +2 7.11 orf00026 12681 12505 -1 0.96 orf00027 13564 13256 -2 7.28 orf00028 14057 13569 -3 9.56 orf00030 14432 14217 -3 8.97 orf00032 15138 14503 -1 8.88 orf00033 15280 15396 +1 0.08 orf00034 15555 16310 +3 7.73 orf00035 16536 16967 +3 5.36 orf00036 17001 17426 +3 12.93 orf00037 17512 17784 +1 5.96 orf00038 17809 18414 +1 7.06 orf00039 18886 19242 +1 8.09 orf00040 19252 19623 +1 10.59 orf00041 19825 20736 +1 9.48 orf00042 20743 21177 +1 10.57 orf00043 21208 21321 +1 5.16 orf00044 21577 22128 +1 12.77 orf00045 22389 23558 +3 8.26 orf00046 23638 23838 +1 12.55 orf00047 23968 24135 +1 11.86 orf00049 24214 24468 +1 10.41 |
Command line arguments
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-seqall] (Parameter 1) |
seqall | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | 2 |
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.kglimmer |
| Additional (Optional) qualifiers | ||||
| -topology | string | liner or circular | Any string | |
| -gencode | integer | 11 | Any integer value | 0 |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
Input file format
kglimmer can use any genome sequence data that seqret can read.Output file format
The output from kglimmer is general Glimmer output file. That has header and 5 column tablar file (orgID, start position, end position, frame, score).Data files
None.Notes
None.References
Delcher, AL., et al.,(1999) Improved microbial gene identification with
GLIMMER, Nucleic Acids Research, 27:23, 4636-4641.
Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with a status of 0.Known bugs
None.See also
| Program name | Description |
|---|---|
| seqret | Reads and writes (returns) sequences |