Finding If A Gene Pair Is Paralogous And Accession Ids

Question

[Angel]

Hello,

What do you recommend is a well tested method to find if a gene pair is paralogous. I have about 200 gene pairs to test so I can't really do it manually.

A friend recommended using accession IDs and using methods similar to blast. If this is the only method, I have three related questions: 1. How and from where do I download all the accession IDs for all the genes? 2. How do I take care of alternative splicing of the genes? 3. Should I simply use sequence similarity e.g. 90% to decide if the genes are paralogous?

Thanks so much in advance.

[ancient_learner]

this may be of some use What is the best method to find orthologous genes of a species? http://www.researchgate.net/post/How_to_detect_paralogs_in_a_list_of_protein_pairs_in_a_high-throughput_manner
http://asia.ensembl.org/info/genome/compara/homology_method.html