MalAvi · release …
MalAvi BLAST
Paste a cytochrome b sequence here and it will be compared to every lineage in the current release of MalAvi using something that is like BLAST. In fact it's similar but still not exactly the same as the DECIPHER based function in malaviR, but it works similarly and gets you the correct comparisons (the most important thing). The name is the one the old shiny app had, because that is what people look for; it is not NCBI BLAST, and the numbers here are not BLAST scores.
This is run through your browser, so by pasting a sequence here you are not uploading it anywhere, it remains private. This is meant to replace the shiny app we were using previously.
Query sequence
Top N hits
Loading the release…
Nothing has been run yet.
Candidates are found by shared 16-mers against the release, then aligned in full (overlap alignment, free end gaps, match +1, mismatch −1, gap −2). The Score column is that alignment's score under this scheme. It is not a BLAST bit score and not comparable to one, and there are no e-values here: every candidate is aligned, and the shortlist is a seed-count cut rather than a significance cut.
A lineage is listed only when at least 50 positions of it align to the query with a score of 30 or more, so the 16-base run that nominated it, plus a few chance matches around it, is never shown as a hit. Finding a lineage at all needs one exact 16-mer in common: a sequence that differs from everything in MalAvi at roughly every sixteenth base, about 6% divergence spread evenly, will not be found here, and is a question for BLAST rather than for this page. Gap characters in the paste are removed before matching and U is read as T.
An ambiguity code (R, Y, N and the rest) on either side is counted as a match when it is compatible with the base on the other side, the same rule the submission checker uses, and never as a difference. The AmbiguousMatches column says how many of a row's matches were counted that way, a percent that includes any is marked †, and those positions are the “:” columns of the alignment.