9.2 References

9.2 References

  • Higgins, D., J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins, T. J. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research 22:4673-4680.

    Main page

    http://www.ebi.ac.uk/clustalw/

    User help

    http://www.ebi.ac.uk/clustalw/clustalw_frame.html

    Download

    ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

    ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/

Chapter 10. HMMER

HMMER is a collection of programs that create a hidden Markov model (HMM) of a sequence family which can be utilized as a query against a sequence database to identify (and/or align) additional homologs of the sequence family. HMMER was developed by Sean Eddy at Washington University. For details, see Section 10.1 at the end of this chapter.

Each program and their respective options are listed below. We're using Version 2.2 of HMMER.

hmmalign Align sequences to an HMM profile.

hmmalign [options] hmmfile seqfile

Options

-h

Print brief help; includes version number and summary of all options, including expert options.

-m

Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states.

-o f

Save alignment to file f instead of to standard output.

-q

Quiet; suppress all output except the alignment itself.

hmmbuild Build a profile HMM from an alignment.

hmmbuild [options] hmmfile alignfile

Options

-f

Configure the model for finding multiple domains per sequence, where each domain can be a local (fragmentary) alignment.

-g

Configure the model for finding a single global alignment to a target sequence.

-h

Print brief help.

-n s

Name this HMM s.

-o f

Re-save the starting alignment to f, in Stockholm format.

-s

Configure the model for finding a single local alignment per target sequence.

-A

Append this model to an existing hmmfile rather than creating hmmfile.

-F

Force overwriting of an existing hmmfile.

hmmcalibrate Calibrate HMM search statistics.

hmmcalibrate [options] hmmfile

Options

-h

Print brief help.

hmmconvert Convert between profile HMM file formats.

hmmconvert [options] oldhmmfile newhmmfile

Options

-a

Convert to HMMER 2 ASCII file.

-b

Convert to HMMER 2 binary file.

-h

Print brief help.

-p

Convert to GCG profile .prf format.

-A

Append mode; append to newhmmfile rather than creating a new file.

-F

Force

-P

Convert the HMM to Compugen XSW extended profile format.

hmmemit Generate sequences from a profile HMM.

hmmemit [options] hmmfile

Options

-a

Write the generated sequences in an aligned format (SELEX) rather than FASTA.

-c

Predict a single majority-rule consensus sequence instead of sampling sequences from the HMM's probability distribution.

-h

Print brief help.

-n n

Generate n sequences. Default is 10.

-o f

Save the synthetic sequences to file f rather than writing them to stdout.

-q

Quiet; suppress all output except for the sequences themselves.