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Query regarding PROJECT SUBMISSION..

Posted: Thu Apr 11, 2013 7:06 pm
by pgupta
Hi

We are trying to complete the word document required for the project submission and had a quick question about the section where we try to make sure that we are not missing out any genes in the fosmid.So we take the predicted protein sequence for the predicted genes on the fosmid which do not align with any of the blastX hits and perform a blastP against the nr protein database.We get a significant ht of 1e-37 and a few more values which are lower than 1e-5 but they are not for genes in drosophila.When we perform the balstP against nr protein database for only drosophila taxa we get a bad e value of 0.24.

In such a case do we just take a screenshot for the blast results which give us significant hits with genes from other organism and just say that we do not get genes with significant hits in drosophila or do we need a seperate screenshot with blast results specifically for drosophila?

Thanks
paromita

Re: Query regarding PROJECT SUBMISSION..

Posted: Thu Apr 11, 2013 8:05 pm
by wleung
One of the main reasons to perform the blastx search is to identify genes that might be found in other species but not in D. melanogaster. Consequently, you should include the results of the blastx search against all the species. However, you do not need to include a screenshot of the blastx result against only genes in the other Drosophila species.

In addition to performing the blastx search, you should also provide an explanation of all the significant hits (e.g. the blastx hit with E-value of 1e-37) in the blastx results and justify why the feature is not annotated as a gene. For example, if all the significant matches are to hypothetical proteins (e.g. proteins with accession numbers that begin with "XP_"), then we would not annotate the feature as a gene in order to avoid propagating errors in the computational predictions.