Question: BLAST - annotate package?
6.1 years ago by
Tim Smith • 1.0k
Tim Smith • 1.0k wrote:
Hi, Sorry for this basic question - I'm new to BLAST! I am trying to do BLAST (dna-nucleotide) for a sequence. I want to a sequence with the rhesus organism. I would like to get the following values: 1. Score (bits) 2. E-value 3. # Matches I am trying to use the 'annotate' package with the following code: library(annotate) xx <- blastSequences(x = "CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT",hitListSize=2,program = "blastn") Can (how?) I get the values that I want from the object returned? If not, which package/function should I be using? Also, is there a website where I can get the abbreviations for the databases (e.g. is rhesus = 'rh'?)? Any pointers in the right direction would be highly appreciated many thanks [[alternative HTML version deleted]]
ADD COMMENT • link •