Let's decide here on the status for different tags related to alignment.
There are two groups of questions.
One is related to pairwise and multiple sequence alignments and algorithms. This field is definitely old and it was one of the keystones in the bioinformatics development. You get question like alignment tools supporting codons, RNA alignments editing or full genome alignments.
Of course read alignment is a series sequence alignment steps. In practice, however, most of the current [alignment] questions are specific only to read mapping software, and has nothing to do with sequence alignment methods.
I think we need to think about tags pragmatically, it is a way for people to follow what they are interested in, and clearly these two areas are of interest for different people. In that line, it is worth noting that meta-tags are considered useless and should be avoided.
- If the tag can’t work as the only tag on a question, it’s probably a meta-tag
- If the tag commonly means different things to different people, it’s probably a meta-tag
These are the results from our quite diverse lab, where some people are working with RNA-seq data. Clearly just [alignment] is ambiguous.
In the current form [alignment] is a meta-tag.
Meta-tagging is explicitly discouraged.
I see two ways of dealing with this.
Two separate tags
For the read alignment I propose using [read-alignment] tag. It's unambiguous. Using [alignment] wouldn't be fair because a) sequence alignment preceded read alignment b) some people (including me) still think about sequence alignment by default c) if you search google scholar for "alignment", four out of five top results will be related to sequence alignment.
For the sequence alignment I propose [sequence-alignment]. I wouldn't use [alignment] for the same reason as above (it's ambiguous). [msa] is a poor choice, since msa is considered to be an extension of pair-wise alignment.
Use [alignment] only for the sequence alignment
In this case we have to remove the [alignment] tag from all the read-mapping questions, where the alignment itself is not a problem. Maybe replacing it with [read-mapping] in some cases.
What are your suggestions?
P.S. It goes without saying, that a question related to both read alignment and sequence alignment could be tagged with the both tags. E.g. "Is it practical to use Smith–Waterman algorithm inside XYZ-mapper".