Entering edit mode
20 days ago
William
•
0
Hello Biostars,
I'm currently a new learner in bioinformatics and would like to perform some gene alignment BLAST search. I have chosen a specific gene of interest (lets say the BRCA1 gene) and have performed Nucleotide BLAST search to look for similar and dissimilar genes. However the search result came with a whole list of the same BRCA1 gene with 0.0 E-value. How could I find other genes that was similar with the BRCA1? Also, how could I adjust the parameters so that the BLAST result could include alignments with E-value > 1, indicating that the gene was "dissimilar" with the BRCA1?
Many thanks!
Are you using Blast on the terminal or on the website? If on the website, you have to go to Algorithm parameters > Expected threshold. Although e-values of >1 are pretty much non-informative.
Thanks for your reply! Yes I'm using the BLAST website. Indeed my ultimate goal is to gather some similar genes and some dissimilar genes and mapping them with microarray probe IDs for further cluster analysis. Sadly I've got trapped in finding the associated genes.
I have tried to adjust the threshold value to 1 but it just failed to generate any results (searching error)
while I was still not able to find genes similar with the BRCA1 (all results generated were just other forms of BRCA1...)
Sorry but seems I was to green to this field.
Maybe you are just approaching the problem from the wrong side. You can limit (and I highly encourage you to) your search to a single species (e.g. human, mouse). It will be easier then to obtain other hits for other genes within the same species