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]  

Basic options:
  -h : show brief help on version and usage

Options controlling output:
  -o            : direct output to file , not stdout
  --tblout      : save parseable table of per-sequence hits to file 
  --domtblout   : save parseable table of per-domain hits to file 
  --pfamtblout  : save table of hits and domains to file, in Pfam format 
  --acc            : prefer accessions over names in output
  --noali          : don't output alignments, so output is smaller
  --notextw        : unlimit ASCII text output line width
  --textw       : set max width of ASCII text output lines  [120]  (n>=120)

Options controlling reporting thresholds:
  -E      : report models <= this E-value threshold in output  [10.0]  (x>0)
  -T      : report models >= this score threshold in output
  --domE  : report domains <= this E-value threshold in output  [10.0]  (x>0)
  --domT  : report domains >= this score cutoff in output

Options controlling inclusion (significance) thresholds:
  --incE     : consider models <= this E-value threshold as significant
  --incT     : consider models >= this score threshold as significant
  --incdomE  : consider domains <= this E-value threshold as significant
  --incdomT  : 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  : MSV threshold: promote hits w/ P <= F1  [0.02]
  --F2  : Vit threshold: promote hits w/ P <= F2  [1e-3]
  --F3  : 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         : set # of comparisons done, for E-value calculation
  --domZ     : set # of significant seqs, for domain E-value calculation
  --seed     : set RNG seed to  (if 0: one-time arbitrary seed)  [42]
  --qformat  : assert input  is in format : no autodetection
  --cpu      : number of parallel CPU workers to use for multithreads  [2]