[Bioperl-pipeline] Re: how to annotate contigs

[Elia Stupka]

> Yeh my basic issue is keeping track of annotation features on a contig and
> making sure if I blast the contig I return enough matches to cover it etc...

You are best off with the bioperl pipeline, we should try to give you a
qucik tutorial into it. The easiest way to start is if you download via
CVS all the following code:

bioperl-live
bioperl-run
bioperl-pipeline
biosql-schema

the instructions are at cvs.bioperl.org but basically you do:

cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login
when prompted, the password is 'cvs'

cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl checkout
bioperl-live

and the same for all other above mentioned modules

This will give you the tools you need to run a simple blast pipeline. The
features can be stored in a variety of databases, but for storage and
viewing you are best off with the ensembl schema, which gives you "for
free" a viewer to display hits on the web,etc. To download ensembl via cvs
do this:

cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/CVSmaster login
...password CVSUSER...
cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/CVSmaster co -r
branch-ensembl-4 ensembl

We have XML templates for the bioperl pipeline that we are building for
simple annotation pipelines, and it would be easy to modify one to suit
your needs, so you don't need to get too deep into the code.

> One way our contigs are different than most genome projects is that they
> come from individual clones. We dont  shot-gun clone BACs or other large
> insert clones, we mainly sequence smaller insert clones and then assemble
> them into contigs and from contigs to scaffolds. 
> So I am not sure if ensembl would work as well as the bioperl pipeline.

Absolutely, it doesn't matter which co-ordinate system you use, you can
always map to other coordinate systems.

> Speaking of which, is there any kind of stand alone document for all the
> packages?

There is docs and tutorials for bioperl and some for the bioperl-pipeline,
we had a guy who got the basics done with the docs we provide, so it
should be ok to get started, but we are happy to help.

Elia

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