Talk:Sequence alignment

Pre-2004 adds
Sorry. I rather forged ahead and added a lot of content to this page without suggesting it first. I hope you can forgive me - I was just rather eager to add something on a topic that I know about.

I have taken pains not to remove anything, so if you don't want what I've added it should be easy enough to get rid of my new stuff.

MockAE.

Needs massive software listing update
The software listing is horribly out of date. I'm currently working on benchmarking such aligment packages, and the ones listed here are fast but awful in quality. T-Coffee, Di-Align, MUSCLE, and others merit mention. Davidstrauss

Reverted reference conversion
Tooto helpfully refconverted this page, and I temporarily reverted that change. I meant to put a comment in the article asking people not to change the references, but I figured, what are the odds of someone converting this exact page in the next week or two?

I'm actively working on this article and find it much easier to add the references in the old style first and then use refconvert at the end, so that the reference text isn't interspersed with the article text. So I'll re-convert the references after the text is more complete. Opabinia regalis 03:38, 24 June 2006 (UTC)

old external links section
I removed the external links section from the main article pending their merger with sequence alignment software. For the time being I'm storing them here for easy reference. Opabinia regalis 04:40, 4 July 2006 (UTC)


 * Blast Server at the NCBI


 * Local alignment tools:
 * Smith-Waterman (online): Emboss::WATER (full memory dynamic programming matrix) - SSEARCH - STRETCHER (optimized dynamic programming matrix) - SEQALN
 * Suffix_tree based (fast): REPuter
 * Seed based (online): FASTA - BLAST family - human BLAT
 * Spaced seed based (more accurate): PatternHunter - human BLASTZ - YASS
 * Global alignment tools:
 * Needleman-Wunsch (online): Emboss::Needle (full memory dynamic programming matrix) - Emboss::Matcher (optimized dynamic programming matrix)
 * Suffix_tree based (fast): MUMmer
 * Multiple alignment tools (online): DIALIGN-T - Clustal - Dialign - MAFFT - Multalin - MAVID - Multi-LAGAN - Muscle - POA - ProbCons - T-Coffee


 * An excellent article at the NCBI web site on the methodology of the BLAST algorithm and the statistical significance of sequence alignments in general.
 * JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological pairwise local sequence alignment.


 * Alignment of Genomes with Rearrangement: Mauve - Mulan - Shuffle-LAGAN (pairwise only)


 * Visualisation tools for alignments
 * VISTA genome browser http://pipeline.lbl.gov
 * Mauve visualization system http://gel.ahabs.wisc.edu/mauve
 * STRAP - 3D-alignments and sequence alignments http://3d-alignment.eu
 * Open content directory of sequence alignment resources (BioDirectory)
 * Sequence Alignment

Grammar Suggestion
I'd suggest rearranging this sentence to improve readability: "If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another." GravityIsForSuckers 22:09, 28 August 2006 (UTC)
 * Do you have a suggested rewording? Perhaps removing the parenthetical explanation of indels? It sounds fine to me, but it should, since I wrote that sentence in the first place :) Opabinia regalis 05:03, 29 August 2006 (UTC)
 * It would be easier for me to be more specific (or I would have just changed it myself) if I knew this particular subject matter. Perhaps someone else will have an opinion on this. GravityIsForSuckers 05:29, 29 August 2006 (UTC)
 * How about - The differences in the aligned sequences correspond to mutations that have occurred in one or both lineages since their time of divergence.If two sequences share a common ancestor, mismatches and gaps in the aligned sequences can be interpreted as point mutations or insertion/deletion mutations (indels), respectively. Gribskov 04:04, 20 September 2007 (UTC)

Wording of the lead
The lead has gone through a few changes since this hit the main page. Theuser, I take your point about arranging residues rather than sequences, but the deficiency of the "residues" wording is that it implies that the order of the residues in the sequence is altered, which is more ambiguous than the alternative "arranging primary sequences". Also, the removal of the word "may" or its equivalent in the statement about emphasizing similarity is much too strong. Spurious similarity happens and there shouldn't be an implication that the results are more definitive than they are. Opabinia regalis 00:37, 29 August 2006 (UTC)


 * I'm also confused by the wording "historically similar". Certainly sequence-alignment algorithms don't have any information about history, but just operate on sequences?  Biologists may use sequence-alignment results to make inferences about history, but sequence-alignment itself doesn't look for things that are "historically similar"; rather, it finds things that are similar by some algorithmic metric. --Delirium 01:24, 29 August 2006 (UTC)
 * You're right, I reworded it closer to the original. The algorithms themselves are usually ignorant of history (except some that can use an independently-derived phylogenetic tree as input), but the results are usually interpreted as reflecting evolutionary change. Opabinia regalis 01:33, 29 August 2006 (UTC)
 * Looks better now; thanks! --Delirium 20:05, 31 August 2006 (UTC)

Assessment of significance
I think this section is unnecessarily vague (even for a non-technical audience). I could add a few details here. Also, the discussion of convergence, IMO, makes it sound much more likely than it really is. Patterson (I think) made a compelling argument in a paper sometime in the 80s (again, I think). I could dig this up, or reconstruct it. Gribskov 04:10, 20 September 2007 (UTC)

"Bioinformatics sequence alignment"
I think "bioinformatics sequence alignment" is a horrible name for this page. It showed up on my watchlist and my immediate reaction was "what's that?". If it absolutely has to move, it should go to "Protein and nucleic acid sequence alignment" or something like that. I think the article should stay at "sequence alignment" though. --Aranae 22:26, 24 October 2007 (UTC)
 * Fully agree. The move should at least have been discussed, especially since it is a featured article. Have moved it back to the original name. Shyamal 01:06, 25 October 2007 (UTC)
 * Me three. Thanks, Shyamal. I don't see a compelling reason for this at all; there's no outstanding ambiguity that needs to be resolved by a longer and less intuitive title. Opabinia regalis 02:38, 25 October 2007 (UTC)

Editing
"Semi-conserved": Is that term really defined? It may be specific to how a user sets up the software. I found an article on the internet saying it means having similar shape, so I added that to the first figure's key. Perhaps the idea should be removed from the article & figure.

"Conservation of base pairing" is mentioned. I find no mention in Wikipedia of that, though the internet has around 250 references to it. I suspect that conservation of bases, rather than base pairing, is meant, so I changed base pairing to base pairs.

The distinction between global and local alignments is not spelled out.--Christopher King (talk) 16:45, 8 January 2009 (UTC)

Links only with uppercase "S"
Links to this page only work if the "S" in "sequence" is capitalized. This should be changed so that links work with letters in either upper or lower case. I believe you change the page title to accomplish this. ask123 (talk) 17:02, 5 May 2009 (UTC)

bug in local alignment example
The local alignment example is clearly wrong, since

FTFTALILLAVAV

--FTAL-LLA-AV

will have a higher score with any substitution matrix or gap costs.

Kevin k (talk) 03:17, 17 September 2009 (UTC)

Wish List
I wish there was a clearer distinguishing here between local and global alignment methods. Briancady413 (talk) 14:25, 18 February 2010 (UTC)

Consensus symbols error
There was a little mistake in Consensus symbols definition - "." (semi-conserved substitutions) and ":" (=conserved substitutions) were inverted. But the picture is still wrong and I have no time (and don't know how) to fix it. 80.188.178.177 (talk) 13:56, 19 June 2010 (UTC)

Text representations - CIGAR, VULGAR etc.
I noticed a CIGAR-shaped hole around here, but I'm not sure how to fill it. I made CIGAR string‎ and linked from Cigar (disambiguation)‎. I doubt there is enough material for a whole article, so I made it a redirect. I'm reluctant to edit this article because it was featured (should I be?). -- Silicosaurus (talk) 15:24, 18 April 2012 (UTC)

I'm not an expert, but the leads I have are
 * CIGAR string format
 * is emitted by the Exonerate aligner
 * is used in an extended form by Ensembl
 * There are several specifications, but I was told recently that the SAMtools format has the nearest to a superset of features.
 * Accuracy of the expansion is in doubt, compare Compact Idiosyncratic Gapped Alignment Report, concise idiosyncratic gapped alignment report — Preceding unsigned comment added by Silicosaurus (talk • contribs) 15:38, 18 April 2012 (UTC)
 * VULGAR format is a variation
 * It is used in GFF3

I think if CIGAR string redirects here, then the article should at least mention CIGAR strings. I just searched Wikipedia and was confused by this discrepancy; I thought I must be missing something in the article. Currently this article seems to focus on pairwise alignment (of comparable strings) and multiple sequence alignment, so CIGAR strings are not very relevant. The only representations of alignments discussed in the article currently are those where both sequences are written out. Common methods of representing an alignment to a reference genome are not mentioned.

I feel that this article would benefit from an "Alignment to a reference genome" section which could briefly mention SAM/BAM/CRAM representations and link to the SAM format specification, which covers CIGAR strings. Happy to have a go at this if there is some agreement. Currently I think that there is no description of the SAM/BAM/CRAM file formats on Wikipedia (?), even though there is a SAMtools article, and there are pages on some other bio formats such as GFF or FASTQ. 59.167.191.34 (talk) 03:16, 16 January 2015 (UTC)

Audio Recording
Hi, I created an audio recording for this article. But I wasn't sure how to pronounce some words/acronyms and just made a good guess. I'd appreciate any corrections.


 * MUM
 * Needleman–Wunsch
 * indel
 * Genewise
 * FASTA
 * EMBL FASTA
 * NCBI BLAST
 * BAliBASE
 * SSAP

Thanks. --Mangst (talk) 00:50, 6 June 2012 (UTC)

Shorter paragraphs
This is mostly just so that I'll remember later. I'm in a rush at the moment, but: this article really needs to be split into shorter paragraphs. Risc64 (talk) 03:41, 11 December 2015 (UTC)

External links modified
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