# [alignment], [sequence-alignment], [read-alignment] and [msa] tags

Let's decide here on the status for different tags related to alignment.

There are two groups of questions.

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".

• Please don't downvote this question if you disagree with the proposal. The question is basically asking what to do. If you feel that keeping a single tag and keeping it named alignment is the right option, then downvote my answer, not the question. – terdon Jul 6 '17 at 16:12

I am folding my previous answer, EDIT and comments into this new answer.

1. includes read alignment. This is both conceptually and practically correct. The most widely used read alignment format is SAM, which is an acronym of "Sequence Alignment/Map" format. i.e. SAM is a sequence alignment format. This naming was unanimously approved by the 1000g committee consisting of many top experts in the field. Having worked with various sequence alignments for many years, I simply can't accept we exclude read alignment from sequence alignment.

2. The biggest problem with is that it means different things to different people. Those in phylogenetics may think it means traditional alignment exclusively. Those who have only worked with NGS data naturally think of read alignment. In fact, this tag includes both fields. Forcing this tag to only mean traditional alignment is a wrong thing we should stop populating. It will also lead to confusion to NGS people.

3. A meta tag is an excessively broad or excessively ambiguous tag. Telling excessive broadness and ambiguity is sometimes subjective. An obvious meta tag (e.g. "best practice") can be put on almost all questions without narrowing the questions down to a specific field. Currently, we have two less obvious meta tags and due to excessive ambiguity. does not represent a field in bioinformatics. It could mean text mining or text processing, two distinct fields. Similarly could mean reference genome (I have retagged all questions taking this meaning) or literature, again two distinct topics. Importantly, a tag is not necessarily meta if it can be divided to more specific subfields. Actually, a true meta tag often can't be subdivided because it lacks a clear scope.

4. To me, is not meta because it clearly defines a subfield in bioinformatics. If we think "alignment" is meta, "read-alignment" would be meta, too, because it includes both DNA read alignment and RNA read alignment. I can't just follow read-alignment if I am only interested in RNA-seq. In addition, is frequently a safe fallback tag when the asker is not familiar with the different types of alignment. I predict it would keep popping up with time even if we retagged all current questions.

5. I don't think there is a right terminology for "alignments that are not read alignment" because each other type of alignment belongs to its own field and often uses distinct algorithms (at least partly). I think at the current stage, the best we can do is to create a tag for a smaller category of "traditional alignment". I propose to use "msa" (with "multiple-sequence-alignment" being a synonym) for MSA, "rna-structure-alignment" for RNA structure-aware alignment and "full-genome-alignment" for genome-vs-genome or assembly-vs-genome alignment.

• Conceptually bioinformatics is biology, and why do we need a separate SE? :) From the practical point of view, I suggest you check the questions. They are conceptually very different and most of current [alignment] question have nothing to do with the sequence alignment itself. Also, I explain why msa is not a good choice of tag. Otherwise we should have another one for pairwise alignment, which sounds too specific. – Iakov Davydov Jul 6 '17 at 14:06
• In any case, [alignment] in a current form is a meta-tag. We should do something about it; and introducing msa doesn't solve the problem. – Iakov Davydov Jul 6 '17 at 14:14
• Yes, but not to everyone and tags should be understandable in the same way by everyone irrespective of their subfield. So since alignment can and does mean different things to different people, it isn't a good tag. You are an expert in the field, so of course you understand that read alignment and sequence alignment are essentially the same thing. Others, however, can be confused by this. Plus, the word is so ambiguous that I'm willing to bet we'll end up having people tagging questions about left-aligning variants or even printf output with alignment. – terdon Jul 6 '17 at 18:18
• @user172818 I agree completely that [alignment] is a correct term. But it doesn't make it a useful tag (e.g. I would probably subscribe to [sequence-alignment], but not to [read-alignment]). I know that you have a proficient experience in both, but it doesn't mean everyone does; you can subscribe to both. And again, when read-alignment problem is really boils down to sequence alignment, one can use both tags. Tags are not about ontology, it's about filtering the content. Could you have a look at the blog post on meta-tags? – Iakov Davydov Jul 6 '17 at 20:28
• @user172818 There are two separate issues here: i) whether we should have separate tags for "traditional" sequence alignment and short read alignment and ii) what should those tags be. My main issue here and, I think, Iakov's, is that we need separate tags for the two. What that tag should be is debatable but I feel very strongly that we need to have different tags for these two types of alignment. Now, using sequence-alignment and read-alignment seems the most natural and obvious to me. That doesn't in any way suggest that read alignment is not a form of sequence alignment! – terdon Jul 7 '17 at 7:48
• [cont] Of course reads are sequences and aligning them is a form of "sequence alignment". But that's not what most people would think of when they hear the term "sequence alignment", I think. Most of us would think of Clustal & co and not BWA & co. But we could have another wording if you like. As long as we have two separate tags for it. – terdon Jul 7 '17 at 7:52
• As for alignment by itself, that is a meta tag. The definition is not subjective at all: it is a tag that, by itself, does not define what the question is about and needs a second tag for clarification. "Alignment" is ambiguous. It can refer to aligning NGS reads, whole genomes, proteins, genes, RNA, structural alignments, left-aligning variants. . . And it has meanings outside jargon, in everyday language as well. This is not a good tag. – terdon Jul 7 '17 at 7:54
• @user172818 then let's use different names! All I am really arguing in favor of is to not have a single tag describing "traditional" sequence alignment and NGS-style aligning of reads to a genome. If your objection is only to using the tag sequence-alignment only for the former, then let's use another name for it. How about multiple-sequence-alignment and read-alignment? I would argue against genome-alignment since that could be for aligning genomes, and against msa since that's not very descriptive. – terdon Jul 7 '17 at 12:33

I agree with this. To me the word alignment will always mean aligning sequences to each other and not aligning reads to a genome. Yes, the two are not really different under the hood, but that's not the point. Tags serve two main uses:

1. They make it easier to search for topics;
2. They help experts find questions they are interested in (through marking a tag as a favorite).

Although the underlying methods involved in both multiple sequence alignments and read mapping are not fundamentally different, the tools used for each are. Also, the people interested in each and knowledgeable about each are not always the same. I, for example, am far more familiar with sequence alignment than with aligning reads.

So, given that we have two sets of not necessarily overlapping experts and two different subjects, having two tags makes sense. The tags should serve to clearly mark what a question is about. Tagging something with is not really informative since we don't know what kind of alignment we are referring to. In general, I am in favor of making tags be as descriptive and unambiguous as possible.

I would therefore be in favor of using for multiple sequence alignments using tools like t_coffee of MAFFT and for tools like bwa or bowtie that align reads to a reference. We should then remove the tag since it isn't enough to explain what a question is about by itself.

I don't see an easy distinction between and . It could perhaps be argued that if someone is mapping and aligning lots of reads to a genomic reference, then that's , and if alignment is not being done at the same time (e.g. Kallisto, Salmon), then that's or .