A MULTIPLE ALIGNMENT PROGRAM for syntenic genomic sequences (MAP2):

Copyright (c) 2005
Iowa State University Research Foundation, Inc.
All Rights Reserved

Liang Ye and Xiaoqiu Huang
Department of Computer Science
Iowa State University
226 Atanasoff Hall
Ames, IA 50011-1040, USA

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Last update time 3/15/2004

The program MAP2 is developed based on the algorithm of MAP (Huang, 1994) and
GAP3 (Huang and Chao, 2002). MAP2 computes a global alignment from
homologous sequences from different species. The program takes as input a file
of sequences in fasta format, for example, seq.fasta. Similar regions
are reported in an output file.
   
    To align a set of sequences in file seq.fasta,
    use a command of form
          
map2  seq.fasta  bpenalty  ms  q  r > result
   
    where map2 is the name of the object code, bpenalty is a positive integer
    specifying the major difference. ms is a negative integer specifying mismatch
    weight, q and r are non-negative integers specifying gap-open and gap-extend
    penalties,respectively. Output alignments are saved in the file "result".
                                                                                   
    An example command is
          map2 seq.fasta 250 -12 38 3 > result
                                                                                   
The results are in several files, including the standard output, seqfilename.info,
seqfilename.flat.
                                                                                   
1 standard output
The standard output can be directed to an output file, say seqfilename.out.
The .out file shows alignments of similar regions in plain text.
MAP2 builds alignments in the order of a binary tree based on
pairwise sequence similarity scores. For each node in the tree,
an alignment of similar regions for the corresponding subset of sequences
is reported along with a simple summary including the number of similar regions,
the total alignment length of the similar regions, and the portion of
the alignment with a column consensus percent identity bigger than 75%.

2 .flat
This output file shows alignments in fasta format for each
node in the tree. Each difference section in the alignment is makred by '#'.
The length information for each '#' is stored in the .info file.

3 .info
There are three parts in this output file: (a) the parameter values used in MAP2,
(b) the order of pairwise scores used, and (c) the length information for each
difference section marked by '#'.
            

Ye, L, Huang, X. MAP2: multiple alignment of syntenic genomic sequences. Nucleic Acids Res. 2005 33: 162-170