軟件的下載與安裝教程鏈接 http://www.lxweimin.com/p/39247f589f8a
HMMER 官方下載地址：http://hmmer.org/download.html
HMMER 使用手冊：http://eddylab.org/software/hmmer/Userguide.pdf
#下載 PFAM 數據庫
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfamxx/Pfam-A.hmm.gz
#解壓PFAM 數據庫
gzip -d Pfam-A.hmm.gz
#建立成索引
hmmpress Pfam-A.hmm
#使用 hmmscan 進行 Pfam 注釋
hmmscan -o 1.txt --tblout 1.tbl -E 1e-5 Pfam-A.hmm 1.faa
Usage: hmmscan [-options] <hmmdb> <seqfile>
Basic options:
-h : show brief help on version and usage
Options controlling output:
-o <f> : direct output to file <f>, not stdout
--tblout <f> : save parseable table of per-sequence hits to file <f>
--domtblout <f> : save parseable table of per-domain hits to file <f>
--pfamtblout <f> : save table of hits and domains to file, in Pfam format <f>
--acc : prefer accessions over names in output
--noali : don't output alignments, so output is smaller
--notextw : unlimit ASCII text output line width
--textw <n> : set max width of ASCII text output lines [120] (n>=120)
Options controlling reporting thresholds:
-E <x> : report models <= this E-value threshold in output [10.0] (x>0)
-T <x> : report models >= this score threshold in output
--domE <x> : report domains <= this E-value threshold in output [10.0] (x>0)
--domT <x> : report domains >= this score cutoff in output
Options controlling inclusion (significance) thresholds:
--incE <x> : consider models <= this E-value threshold as significant
--incT <x> : consider models >= this score threshold as significant
--incdomE <x> : consider domains <= this E-value threshold as significant
--incdomT <x> : consider domains >= this score threshold as significant
Options for model-specific thresholding:
--cut_ga : use profile's GA gathering cutoffs to set all thresholding
--cut_nc : use profile's NC noise cutoffs to set all thresholding
--cut_tc : use profile's TC trusted cutoffs to set all thresholding
Options controlling acceleration heuristics:
--max : Turn all heuristic filters off (less speed, more power)
--F1 <x> : MSV threshold: promote hits w/ P <= F1 [0.02]
--F2 <x> : Vit threshold: promote hits w/ P <= F2 [1e-3]
--F3 <x> : Fwd threshold: promote hits w/ P <= F3 [1e-5]
--nobias : turn off composition bias filter
Other expert options:
--nonull2 : turn off biased composition score corrections
-Z <x> : set # of comparisons done, for E-value calculation
--domZ <x> : set # of significant seqs, for domain E-value calculation
--seed <n> : set RNG seed to <n> (if 0: one-time arbitrary seed) [42]
--qformat <s> : assert input <seqfile> is in format <s>: no autodetection
--cpu <n> : number of parallel CPU workers to use for multithreads [2]
