How to find similar sequences by hmmsearch

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Hmmsearch searching for similar sequences

HMMER is a very powerful software package for biological sequence analysis based on hidden Markov model. its general purpose is to identify homologous protein or nucleotide sequences and sequence alignment. Compared with BLAST, FASTA and other sequence alignment and database search tools, HMMER is more accurate.

Hmmsearch is available to find similar sequences in the case of HMM model, and the usage is as follows:

Hmmsearch-domtblout Ensembl.txt PF01535.hmm Zea_mays.AGPv3.24.pep.all.fa

The input file PF01535.hmm is a HMM model. The comparison sequence file can be in FASTA format.

-output in domtblout:domtblout format

The results are sorted by E-values value from smallest to largest, similar to blast.

Where target name is the name of each target sequence

Query name is the name of the query sequence

Score compares scores. The higher the score, the more similar it is.

Expected value of E-value target sequence (statistical significance)

The most important thing is the E-value value, the smaller the value, the more credible it is, which is equivalent to a statistic.

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