gene models

[polijana]

Hello everyone,

I have questions here, I do have a set of predicted gene models (from ~25k assembled contigs)..there are also another set of gene models(from JGI) of different species of the same genus im working with...so, how am i going to compare between these two set of gene models?The one from JGI is n chromosme level but mine only at contigs level. Im interested to know the location of my gene models with refer to the pseudochromosme at JGI. Thnks

[mike.t]

JGI should provide a mapping file that shows the order of the contigs in the pseudochromosome. you need to write a program (Perl, Python etc) to convert your contig level coordinates to the pseudochromosome coordinates.

Are the JGI models available in contig coordinates from some other database? GenBank perhaps?

3rd option - align the transcripts of models to the pseudochromosome using a spliced aligner. this could introduce errors though, especially with duplicated genes

[polijana]

thanks mike, apreciate it