Hmmer 사용법 - 리눅스

http://hmmer.org/ 사이트에 접속해서 파일을 다운로드합니다. 

HMMER

 

 

Hidden Markov Model을 이용한 알고리즘으로 phmmer를 사용하여 데이터베이스에 대해 단백질 질의 시퀀스를 검색하거나 jackhmmer를 사용하여 반복 검색을 수행할 수 있습니다.

 

 

hmmbuild build profile from input multiple alignment

hmmalign make multiple sequence alignment using a profile

hmmsearch search profile against sequence database

hmmscan search sequence against profile database

hmmpress prepare profile database for hmmscan

phmmer search single sequence against sequence database

jackhmmer iteratively search single sequence against database

nhmmer search DNA query against DNA sequence database

nhmmscan search DNA sequence against a DNA profile database

hmmfetch retrieve profile(s) from a profile file

hmmstat show summary statistics for a profile file

hmmemit generate (sample) sequences from a profile

hmmlogo produce a conservation logo graphic from a profile

hmmconvert convert between different profile file formats

hmmpgmd search daemon for the hmmer.org website

hmmpgmd_shard sharded search daemon for the hmmer.org website

makehmmerdb prepare an nhmmer binary database

hmmsim collect score distributions on random sequences

alimask add column mask to a multiple sequence alignment

 

 

 

globins45.fa (fasta) 예제를 이용하여 hmm 알고리즘을 적용하는 방법입니다. 

우분투에서 진행합니다. 

 

 

hmmsearch globins4.hmm globins45.fa

 

 

hmmbuild globins4.hmm globins4.sto

./hmmbuild globins4.hmm globins4.sto

./hmmsearch globins4.hmm uniprot_sprot.fasta > globins4.out

tar -zxvf uniprot_sprot.fasta.gz

tar -zvf uniprot_sprot.fasta.gz

tar -zxf uniprot_sprot.fasta.gz

./hmmsearch globins4.hmm uniprot_sprot.fasta > globins4.out

 

./phmmer tutorial/HBB_HUMAN uniprot_sprot.fasta

./phmmer tutorial/HBB_HUMAN uniprot_sprot.fasta > HBB_HUMAN.txt

./phmmer tutorial/covid19_aligned uniprot_sprot.fasta > covid19_a.txt

./hmmer tutorial/covid19_aligned uniprot_sprot.fasta > covid19_a_hmm.txt

./hmmbuild tutorial/covid19_aligned uniprot_sprot.fasta > covid19_a_hmm.txt

./hmmsearch tutorial/covid19_aligned uniprot_sprot.fasta > covid19_a_hmm.txt

./jackhmm tutorial/covid19_aligned uniprot_sprot.fasta > covid19_a_hmm.txt

./jackhmmer tutorial/covid19_aligned uniprot_sprot.fasta > covid19_a_hmm.txt

 

hmmbuild globin.hmm globins50.msf

./hmmbuild globin.hmm globins50.msf

./hmmbuild globin.hmm ./tutorial/globins50.msf

 

 

./hmmbuild globin.hmm globins50.msf

 

./hmmbuild covid.hmm covid_pangolin.msf

./hmmbuild globin2.hmm globins50_2.msf

./hmmbuild covid.hmm covid_pangolin.msf

./hmmbuild globin2.hmm globins50_2.msf

./hmmbuild covid19.hmm ./tutorial/covid19_aligned.fasta

 

hmmcalibrate covid19.hmm

./hmmcalibrate covid19.hmm

./hmmsearch covid19.hmm uniprot_sprot.fasta

./hmmsearch covid19.hmm uniprot_sprot.fasta > covid19_hmm_uni.txt

./hmmsearch covid19.hmm swissprot