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Comparison of gene structure

Comparative genomic ORFs ORF structure

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#1 Freemason

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Posted 20 December 2011 - 09:46 AM

Hello everyone,

I have two genomic sequences, and I would like to know if there is any relationship between them regarding the protein coding genes (same proteins?, same order?). They definitely contain mutations on the nucleotide level, so a simple nucleotide BLAST with two sequences as queries is a bit pointless. They are already annotated, so I could theoretically check the corresponding Genbank-Files and look up each and every entry there and do protein BLASTs with the sequences, but that would "a bit" tedious. Moreover, I don't trust automated annotations. My question therefore is: does anybody know a good program that translates two sequences in all reading frames and compares the results?

Thanks for suggestions in advance!

Greetings
Freemason

#2 bob1

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Posted 20 December 2011 - 11:48 AM

Have a look at the UCSC BLAT site, they do alignment of genomic fragments.





Also tagged with one or more of these keywords: Comparative genomic, ORFs, ORF structure

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