[Bioperl-l] AlignIO and Gbrowse_syn

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Aug 11 17:31:32 EDT 2010

I know there was some brief discussion about .maf format a few weeks ago but I've had an enquiry (as below) from a colleague. 
If GBrowse_syn is using .maf format, does AlignIO need more work?
Any comments?


I'd like to plug LASTZ alignments into GBrowse_syn. LASTZ can produce a limit number of alignment formats (http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#options_output). GBrowse_syn accepts clustalw format plus "other commonly used formats recognized by BioPerl's AlignIO parser" (http://gmod.org/wiki/GBrowse_syn_Database) .  Since LASTZ doesn't produce clustalw, I've tried parsing LASTZ maf output to clustalw (and other alignment formats) using AlignIO, however I run into the following issues:
*Strand info is lost (probably fair enough, since this isn't part of the clustalw format per se; incorporating strand info within sequence IDs is a GBrowse_syn clustalw specification)
*The coordinate system for reverse strand matches  differs between LASTZ .maf and BioPerl .maf: for LASTZ, coordinates relate to the reverse complemented sequence, whereas for BioPerl/GBrowse, coordinates relate to the original (non-rev complemented) sequence. E.g. a coordinate of "1" in the LASTZ .maf file refers to the last base of the original sequence; AlignIO prints "1" to the output clustalw file, but since strand info is lost it is construed as the first position at the very start of the original sequence. As a result all reverse match coordinates in the resulting clustalw output file are incorrect.
*AlignIO is unable to parse multiple, individual aligned regions within the same .maf file; it interleaves them

I would be interested to hear whether anyone has already found a solution to integrating LASTZ and GBrowse_syn... and also whether any development of AlignIO to improve support of maf format is planned.
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