HMMER 的使用

软件的下载与安装教程链接 https://www.jianshu.com/p/39247f589f8a
HMMER 官方下载地址：http://hmmer.org/download.html
HMMER 使用手册：http://eddylab.org/software/hmmer/Userguide.pdf

#下载 PFAM 数据库
wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfamxx/Pfam-A.hmm.gz
#解压PFAM 数据库
gzip -d Pfam-A.hmm.gz
#建立成索引
hmmpress Pfam-A.hmm
#使用 hmmscan 进行 Pfam 注释
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]