[WashU] HMMER
User's Guide


| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC|
| Eddy lab | Internal (lab only) | HMMER | PFAM | tRNAscan-SE | Software | Publications |

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Maintaining multiple alignments with hmmalign

Another use of profile HMMs is to create multiple sequence alignments of large numbers of sequences. A profile HMM can be build of a ``seed'' alignment of a small number of representative sequences, and this profile HMM can be used to efficiently align any number of additional sequences.

This is in fact how the PFAM database is updated as the main SPTREMBL database increases in size. The PFAM seed alignments are (relatively) stable from release to release; PFAM full alignments are created automatically by searching SPTREMBL with the seed model and aligning all the significant hits into a multiple alignment using hmmalign.

For example, to align the 630 globin sequences in globins630.fa to our globin model globin.hmm, and create a new alignment file called globins630.ali, we'd do:




> hmmalign -o globins630.ali globin.hmm globins630.fa

hmmalign - align sequences to an HMM profile
HMMER 2.0 (June 1998)
Copyright (C) 1992-1998 Washington University School of Medicine
HMMER is freely distributed under the GNU General Public License (GPL).
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HMM file:             globin.hmm
Sequence file:        globins630.fa
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Alignment saved in file globins630.ali

Using the -o option to specify a save file for the final alignment is a good idea; else, the alignment will be displayed on the screen as output (and an alignment of several hundred sequences will give a fairly voluminous output).


next up previous contents
Next: Introduction Up: Tutorial Previous: Searching a query sequence


Direct comments and questions to <eddy@genetics.wustl.edu>