[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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Introduction

You discover a new protein sequence family, and carefully construct a multiple sequence alignment. Your family, like most protein families, has a number of strongly (but not absolutely) conserved key residues, separated by characteristic spacing. You wonder if there are more members of your family in the sequence databases, but the family is so evolutionarily diverse, a BLAST search with any individual sequence doesn't even find the rest of the sequences you already know about; you're sure there are some distantly related sequences in the ``noise''. You spend many pleasant evenings scanning weak BLAST alignments by eye to find ones with the right key residues are in the right places. You sure wish there was a computer program that did this better.

You get the sequence of another favorite protein and eagerly BLAST it against the NCBI server, and nothing significant shows up. It looks like you'll get no easy information from the sequence.

You BLAST another favorite sequence against the NCBI server; a thousand hits come back, and the top hundred are hypothetical sequences from genome projects. It looks like you'll have to wade through a lot of BLAST output to find the informative hits.

Another sequence comes back a slew of hits to receptor tyrosine kinases, but before you decide to call your sequence an RTK homologue, you recall that RTK's are, like many proteins, composed of multiple functional domains. Is your sequence really an RTK? Or is it a novel sequence that also happens to have a protein kinase catalytic domain, fibronectin type III domain, or immunoglobulin superfamily domain?

These (and other problems in sequence analysis) are the kinds of problems that HMMER tries to address.



 
next up previous contents
Next: Profile HMMs Up: HMMER 2.1 User's Guide Previous: Maintaining multiple alignments with


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