comparative_genomics_related_things

bioinformatics, wga    

MUMmer 序列比对

详见 TheMUMmer3manual

1.比对: nucmer/promer

nucmer/promer [options] <Ref> <Query>

参数： (Ref 和 Query 都可以是多序列)

-maxmatch 不考虑unigueness，可得到更多匹配
-c <int>    设置最小匹配簇,nucmer默认是65,promer默认20
-g <int>    设置相邻matches的最大gap值,n默认90,p默认30
-p <string> 输出文件前缀,默认是out,输出文件为out.delta

2.比对结果的展现:

  1. show-coords -c -d -l -L<int> -I<float> -r <比对结果文件.delta> > <输出文件>

-c: 包含覆盖度
    -d: 包含比对方向
    -l: 包含ref和query长度信息
    -I<float>:  限制呈现的最小的identify
    -L<int>:    限制呈现的最小长度
    -q: 按照query ID和坐标排序
    -r: 按照Ref ID和坐标排序   
    -T: 输出结果用tab分割
    注: 如用于后续的mapview,则必须加上-c -r -l这三个参数
    更多参数用-h查看

  1. show-aligns <比对结果.delta> "某条Ref ID" "某条query ID" > XXXXX.aligns

     #查看两条序列比对情况
 -q/-r   同上
 -w int  Set the screen width - default is 60
 -x int  Set the matrix type - default is 2 (BLOSUM 62),
 other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
 note: only has effect on amino acid alignments

LastZ

lastz sequence1.fasta sequence2.fasta

常用参数设定

详见: 官方帮助文档

  • gfextend/nogfextend Perform/Skip gap-free extension of seeds to HSPs (high scoring segment pairs)

  • chain/nochain

    Perform/Skip chaining of HSPs.

  • gapped/nogapped

    Perform/Skip gapped extension of HSPs.

  • format

    Output format. Type <general> performs a tabular file. detail

  • ambiguous=n

    Treat each N in the input sequences as an ambiguous nucleotide. Substitutions with N are scored as zero.

  • ambiguous=iupac

    Treat each of the IUPAC-IUB ambiguity codes (B, D, H, K, M, R, S, V, W, Y as well as N) in the input sequences as a completely ambiguous nucleotide. Substitutions with these characters are scored as zero.