[BioRuby] GSoC: MAF parser questions

[Raoul Bonnal]

Hi Clayton,
Welcome.

On 26/03/12 09.26, "Clayton Wheeler" <cswh at umich.edu> wrote:

> Hello,
> 
> I'm Clayton Wheeler, an undergraduate microbiology student at the University
> of Michigan. I'm particularly interested in molecular biology and microbial
> ecology, but in a previous life I was a programmer and system administrator
> for 11 years, so I'm very interested in applying that background to
> bioinformatics, also. The lab I've been working in uses bioinformatics tools
> and next-generation sequencing quite a bit, especially for studying
> hydrothermal plume communities; I've been working on the wet-lab side, but
> this is an area I'd like to learn more about. Moreover, I've been using Ruby
> for the last six years or so, and so I'd like to help develop it as a
> bioinformatics platform. The GSoC projects for BioRuby caught my eye, and I'd
> like to see if there's a good way I could contribute there.
> 
> The parser projects for MAF and GFF3 seem interesting and doable; I've been
> looking into the MAF parser project in particular, and I have a few questions
> about it. 
> 
> First, does the set of operations on MAF data described in Blankenberg et al
> (http://1.usa.gov/GQRYvX) cover the use cases that such a parser and indexing
> system should support?
Yes, I think that having all those features implemented will be great. Maybe
it would be better if you define a priority list of all the features.
> 
> Is https://github.com/polyatail/biopython the correct location of the
> BioPython MAF code described in
> http://biopython.org/wiki/Multiple_Alignment_Format? (It looks like it's been
> 11 months since the last commit.)

>From Peter:" Yes, specifically this
branch:https://github.com/polyatail/biopython/tree/alignio-maf

This is something we're going to be looking at merging for Biopython 1.60,
http://lists.open-bio.org/pipermail/biopython-dev/2012-February/009384.html

Peter"


Specs: http://genome.ucsc.edu/FAQ/FAQformat.html#format5

Some MAF app http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
 
> Also, I've found a few existing tools for working with MAF files such as the
> scripts shipped with bx-python and PHAST, but not too many worked examples of
> how they'd be used in practice. Are there any more or less real-world examples
> available of MAF operations demonstrating the kinds of indexed access, large
> data sizes, etc. that should be supported in bio-alignment?
This is an application which uses MAF as input
https://github.com/mlin/PhyloCSF/wiki


--
Ra