【4.5.3】宏基因组基因识别--MetaGeneMark

预测的范围是细菌和古菌(网页版：) 下载地址

使用方法参照上面的metageneannotator和解压缩后的readme。
Example 1:
gmhmmp -m MetaGeneMark_v1.mod sequence.mfa 
Predictions will be in file "sequence.mfa.lst" in default GeneMark.hmm format 

Example 2:
gmhmmp -a -d -f G -m MetaGeneMark_v1.mod -o sequence.gff sequence.mfa
Predictions will be in file "sequence.gff" in GFF format
with nucleotide and protein sequences for each predicted gene. 
其中为sequence.gff生成文件，sequence.mfa为输入文件

Example 3:
after step Example 2
nt_from_gff.pl < sequence.gff > nucleotides.fasta
Nucleotide sequence of predicted genes will be saved in 
FASTA formatted file nucleotides.fasta
注意上面的是一个perl脚本，所以输入文件的< >是不可少的。

Example 4: 
step Example 2
 aa_from_gff.pl < sequence.gff > proteins.fasta
Amino acid sequence of predicted genes will be saved in 
FASTA formatted file proteins.fasta
其中为sequence.gff输入文件

参数介绍：

/sam/metagenemark/gmhmmp  
prokaryotic GeneMark.hmm version 2.10    
Usage:</strong>
gmhmmp [parameters ...] [sequence filename]
Sequence file in FASTA format can have multi-FASTA sequence   

Required parameters:</strong>
-m [filename] File with gene finding parameters    

Optional parameters:  
*** Output options 
 -o [filename] Output file name default = [sequence filename].lst
-a Show protein sequence of predicted genes
-d Show nucleotide sequence of predicted genes
-f [L|G] Output format: [L] LST or [G] GFF2 default = L
-K Show RBS location and score
-k Show RBS scores and spacer; this option must be first in command line   

*** Prediction options</strong>
-r Use RBS for gene start prediction
-s [d|r|.] Strand to predict genes on
default = '.' predict genes on both strands
-p [1|0] Gene overlap are allowed [1] or prohibited [0]
default = 1  [0] is used for gene finding in intron-less eukaryotic genomes
-e [filename] use this file with external infromation to profile predictions     

*** Developer options 
-i [number] Probability of initiation and termination in non-coding state   default = 0.5
-n Turn OFF prediction of the incomplete genes   at sequence gaps: strings of unknown letters 'N'  

Examples:</strong>
gmhmmp -r -m bsub.mod -o sequence.lst sequence.fasta;
gmhmmp -r -p 0 -m yeast.mod -o sequence.lst sequence.fasta 

/sam/metagenemark/gmhmmp -a -d -f G -m /sam/metagenemark/MetaGeneMark_v1.mod -o sequence.gff contig.fasta