Hi, can anyone help me out to understand results of blastx when we get something like this
Query 2469 ASIFNEMNIDPFVVSDKICPKWGKLFV----DeksiseeeceaegkkkckiLNTSVHPKL 2636 +SI NEMN+D + D+ K+F +E S+ E++ + + KK C LN V K Sbjct 1472 SSICNEMNVDLSLEEDE------KMFTNGVDEENSMLEKKLDHKSKKNCSKLNRKVFTKS 1525
here "eksiseeeceaegkkkcki " why these characters are in small letters and gray color? is it specifying anything unusual? Thanking in anticipation Madiha
1 answer
You are seeing the result of automatic filtering of your query for low-complexity sequence. This filter is on for the BLASTN pages to prevent matches that are probably artifacts. The filter substitutes any low-complexity sequence with lowercase grey characters. This allows you to see the sequence that was filtered instead of the "X"s and "N"s of the previous BLAST output. https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#lowercase
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oh right, got it...
Thank you MIttu