-
Anyone up to getting Needleman-Wunsch and Smith-Waterman written in cython? The current all-python versions in pyCogent are super slow and the nwalign package has a severe memory leak issue.
-
To solve #31 and #56, we should create an `AlignmentRecord` or so class (or something like that). The idea is that objects of this class represent the information from one row in a SAM/BAM file, and t…
-
For the use case of finding oligonucleotide binding sites (e.g., PCR primers) it may be preferable to find the best alignment without gaps. Sometimes two similar alignments differ by a gap instead of …
-
It looks to me that SortMeRNA consistently output wrong coordinates in the blast format when the alignment runs across the end of the subject sequence (rRNA).
Assume we have a read of length 150, w…
-
We get a few questions on how to do fuzzy matching with Vespa. Current support for 'fuzzy' is through:
- Regular expressions, only exposed through YQL query syntax using 'matches' instead of 'conta…
-
As best as I can tell by testing with the Python wrapper, the gap extension penalty is not actually used when calculating alignment scores. Instead, the "opening penalty" is assessed against each gap…
-
Hi,
Were external libraries such as [parasail](https://github.com/jeffdaily/parasail) or [striped smith waterman](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library) considered? The…
-
Here are some remarks I had while reading your paper. I'm bundling them in a single issue. Feel free to disagree with them though, and I may well be wrong myself once or twice; some others of these wi…
-
Somewhere between lines 597 and 633, but I'm having trouble narrowing it down further. It seems like it gets into an infinite (or very slow) loop for a few seconds before segfaulting. To reproduce (ye…
-
Using the third sequence from the [100k_illumina1.fastq.gz](../blob/master/demo/100k_illumina1.fastq.gz) and the [Virus_genome.fa.gz](../blob/master/demo/Virus_genome.fa.gz), match of 5, mismatch of 4…