Talk:FASTA format

message: I removed most of the useless and distracting references to comments in the FASTA file because no one supports them and haven't for over 15 years.  For details, see my research -- Andrew Dalke
Not true, comments starting with a semi-colon are supported for instance by the function read.fasta in the seqinR package and by the function readFASTA in the Biostrings package. 90.42.8.116 (talk)
Okay, then "almost no one".  Who publishes/provides data in FASTA format with comments?  What was the driving motivation for adding that support?  Where's the push for Bioperl and other tools to support it? -- Andrew Dalke
As scientists we care about backward compatibility, which is essential for reproducibility. The fact that new tools such as Bioperl (or other recent me-too products in the bioinformatic world) do not support reproducibility is by no way a good argument to remove the documentation about the original format, which is sourced. This is Wikipedia, not Bioperl point of view. 90.48.97.179 (talk) 21:28, 4 February 2009 (UTC)
thread_title: Comments in a FASTA record

message: Looks like the text under "Format" is copied from the NCBI website.  Either that, or the NCBI copied from here.  Does this need to be changed?  —Preceding unsigned comment added by 128.193.214.112 (talk) 22:07, 3 October 2007 (UTC)
replies: text: The NCBI website, however, is a US Federal Government website...and, as it is the author of the appropriate text, it is public domain. However, it should be cited as being such. --AEMoreira042281 15:19, 8 November 2007 (UTC)
thread_title: Copyright?

message: I suggest moving this addition on HUPO-PSI Format to another page, as it confuses the
basic article, and opens the door to n other detailed sequence record proposals.
This is very worthy as a new sequence format proposal, but it is not Fasta format. HUPO-PSI 
is one of several variants that have been proposed or built to bring documentation and
record structure back into Fasta (which was designed for its simplicity). It would be worth
referring to other such formats in this article. NCBI's defline format the current most common variant of Fasta. Add why FastA isn't the solution to documented, structured sequence records.
Dongilbert (talk) 02:47, 18 February 2008 (UTC)
thread_title:  HUPO-PSI Format to another page 

message: I'm not sure if this the appropriate place for this, but I just wanted to say that as a molecular biology student I found this article extremely useful and very reader friendly. Cheers everybody, great work! --Ar-Pharazôn (talk) 19:34, 24 June 2009 (UTC)
thread_title:  Great page 

message: The first section ("Format") contains the following line:
"-- If FASTA files can contain multiple sequences, as suggested by the text below, that is a critical part of the format specification and should be described up front here please. If they cannot contain multiple sequences, this point should be clarified here."
However, right above that, the main text addresses that very question. 
"The sequence ends if another line starting with a ">" appears; this indicates the start of another sequence. A simple example of one sequence in FASTA format [follows]:" (emphasis mine)
This seems crystal-clear to me; in fact, the question is the most jarring part of the section. I'm tempted just to remove the question/comment, but I'm new around here so I don't want to overstep!
Jdrum00 (talk) 05:36, 2 September 2009 (UTC)
thread_title:  Strange comment/question in first section 

message: I thought it'd be helpful to add more information on file extensions in the form of the table.  If I stepped on any toes I wanted to discuss it, so I started this discussion section. Lskatz (talk) 20:55, 28 February 2010 (UTC)
replies: text: I concur. Currently I work with .fa files provided by someone else. I was surprised because .fa is not listed on Wikipedia. Perhaps .fa should also be added? 193.171.188.3 (talk) 10:11, 11 February 2014 (UTC)
thread_title:  Extensions 

message: Do the letters F.A.S.T.A stand for anything ? What is the origin of the abbreviation ? XApple (talk) 10:47, 28 May 2010 (UTC)
replies: text: Before FASTA there were FASTN and FASTP, and I presume papers for them. In the years since I have known about them, I don't remember seeing anything about the acronym, but then again, I wasn't looking. Gah4 (talk) 15:07, 2 May 2018 (UTC)
thread_title: Origin of the name

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thread_title:  External links modified 

message: fastA is not an acronym, It should not be written in upper case.  — Preceding unsigned comment added by SaraCubillas (talk • contribs) 13:41, 4 January 2017 (UTC)
replies: text: Someone above indicates that it might be an acronym. The unix versions that I know of the program are called fasta, where case is significant. How is it written in the original papers? Seems to be all caps there. Gah4 (talk) 15:10, 2 May 2018 (UTC)
thread_title:  Change to lower case fastA 

message: : Thanks for bringing this here. A new paragraph was added regarding FASTA file manipulation with mention to user user-friendly online tools Tomsauv (talk) 14:30, 4 May 2018 (UTC)
thread_title:  Brought over from [[FASTA]].   Should it go into this article? 

message: There is no discussion of interleaved/sequential FASTA format on the page, which could be added.
A section discussing tools available for the sorting of multiple FASTA files/ or popular FASTA utilities could be added.
: You are welcome to add whatever information you think would benefit the article. Natureium (talk) 00:54, 3 May 2018 (UTC)
replies: text: I worked with FASTA files for many years, but not so recently.  The format as I knew it, I believe from the actual FASTA program, allows for multiple lines of sequence data, that are supposed to be the same length, except for the last one, which can be shorter.  That definition allows for the whole sequence on one line.  Interleaved does not seem to apply here, in the usual meaning of the word.  Gah4 (talk) 04:54, 3 May 2018 (UTC)
replies: text:  Reorganized sections and subsections in a more logical way where needed. Added information about sequential and interleavedTomsauv (talk) 14:31, 4 May 2018 (UTC)
thread_title:  sequential/interleaved 

message: Both sections seem to exclusively use references from the same few researchers, and their wider relevance/notability is unclear (and isn’t made clear in the text). This seems little more than self-promotion. Notably, the section about compression also fails to mention the (extremely widespread) utility of gzip compression for FASTA, which makes it very misleading. I recommend either removing the sections or improving them by including a statement explaining the relevance, and referencing independent reviews. I won’t do this myself due to a (very indirect) conflict of interest regarding this topic. klmr (talk) 14:49, 5 February 2021 (UTC)
thread_title:  Compression & Encryption 

message: The article currently states "Hence, 80 characters became the norm.". Although this is quite possibly true, we should
refer to some older discussion or entry or email or mail by people back then who designed the initial FASTA format.
I am finding FASTA files that do not care much at all about the 80 characters limit; some seem to prefer 76. It would
be nice if we could have some kind of reference to some "standard", or if that is not possible, to refer to what
the "most commonly width" was in FASTA. 2A02:8388:1641:5500:8207:8CE:DF2:AB90 (talk) 16:58, 3 December 2022 (UTC)
thread_title:  Default width