How To Retrieve Hmmsearch Output Sequences From Target Database..

Question

[chevivien]

Hallo...how do you retrieve hmmsearch sequences output from target database...for example i have hhmsearch output like one below...and i want to retrieve the sequences from local target data database

# hmmsearch :: search profile(s) against a sequence database

HMMER 3.0 (March 2010); http://hmmer.org/

Copyright (C) 2010 Howard Hughes Medical Institute.

Freely distributed under the GNU General Public License (GPLv3).

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query HMM file: muscle.stockholm.hmm

target sequence database: IRGSP-1.0_protein_2013-04-24.fasta

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Query: muscle [M=1139] Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1017.2 26.8 2.3e-236 788.9 16.6 2.0 2 Os08t0539700-01 NB-ARC domain containing protein. 3.4e-298 993.6 39.1 1.4e-236 789.6 13.2 2.0 2 Os08t0539400-01 Similar to Resistance protein T10rga2-1A. 8.7e-295 982.4 45.4 7e-270 899.9 7.0 3.7 2 Os06t0707733-00 Disease resistance protein domain containing 1.1e-284 949.0 40.4 3.8e-281 937.2 28.0 2.9 1 Os07t0141900-00 Similar to OSIGBa0148A10.13 protein. 3.3e-279 930.8 54.0 8.1e-263 876.5 13.2 3.5 2 Os12t0481700-00 Disease resistance protein domain containing 3.3e-279 930.8 54.0 8.1e-263 876.5 13.2 3.5 2 Os12t0482100-00 Disease resistance protein domain containing 8.1e-278 926.2 79.7 1.3e-247 826.1 21.9 4.1 4 Os08t0296700-01 NB-ARC domain containing protein. 6.1e-277 923.3 25.7 2.3e-255 851.8 16.3 2.0 2 Os03t0579200-00 Similar to NB-ARC domain containing protein. 6.9e-277 923.1 45.3 2.7e-264 881.4 11.1 2.8 2 Os12t0481400-00 Similar to NBS-LRR disease resistance protei 1.1e-269 899.2 7.7 7.6e-212 707.7 18.5 3.0 2 Os11t0598500-00 NB-ARC domain containing protein. 7.6e-266 886.5 52.9 1.1e-250 836.3 9.5 3.4 2 Os11t0429100-00 Hypothetical conserved gene. 1e-264 882.8 19.8 1.4e-261 872.4 13.7 3.5 1 Os11t0598300-00 NB-ARC domain containing protein. 6.3e-261 870.2 32.5 2.2e-174 583.6 14.7 2.1 2 Os08t0246300-01 NB-ARC domain containing protein. 1.1e-254 849.5 19.5 1.5e-254 849.1 13.5 1.0 1 Os12t0564800-01 NB-ARC domain containing protein. 2e-254 848.7 18.3 2.5e-254 848.4 12.7 1.0 1 Os06t0158300-01 NB-ARC domain containing protein. 2.5e-254 848.4 50.1 1.8e-251 838.9 20.9 2.1 2 Os05t0492200-01 NB-ARC domain containing protein.

Answer 1

[5heikki]

Check the esl-tools that ship with hmmer.

Answer 2

[kabir.deb]

Hello chevivien,

Have you solved the problem? I'm facing the same problem and couldn't find any way out. It will be an immense help for me if you please give me suggestions to overcome it.

Thanks in advance

Answer 3

[michau]

If you installed hmmer manually you have esl tools installed as well. There's handy program called esl-sfetch which does exactly that. It's also easy to use. https://cryptogenomicon.org/2011/05/03/extracting-hmmer-results-to-sequence-files-easel-miniapplications/ If you don't have it on your machine already then install hmmer from source http://hmmer.org/download.html