Talk:Sequence analysis

message: I partially rewrote the second paragraph to make it read better.  However, the paragraph seems more appropriate at sequence alignment. Sequence analysis has a much broader scope of tools. Suggest this paragraph is removed and rewritten to do this. Fergycool (talk) 18:41, 22 January 2009 (UTC)
thread_title: Untitled

message: I rewrote the Methodology section and created a Sequence Alignment section. I think both sections need some clean up. It's be nice to have:
* Some citations
* A table that lists and describes some pairwise/multiple sequence alignment methods
* A bit more details about the methods associated with sequence analysis. I can probably get a few examples for say SVM's, HMM's, and etc. Adding a list (or table) of algorithms being used would be nice too. We can have something like:
:*Algorithm type  (tab)  Usage
:*Network Flow  (tab)  Genome assembly, ....
:*HMM   (tab)  Sequence analysis, motif prediction, ... 
Bobthefish2 (talk) 06:00, 20 February 2011 (UTC)
replies: text: Wow... a senior investigator from Sanger. Yes, that sounds reasonable. Presumably, you are very familiar with each of these areas? --Bobthefish2 (talk) 17:24, 17 June 2011 (UTC)
replies: text: I made a few changes - namely collapsing the sequence alignment sections into one. I think it may be a good idea not to describe the individual methods because we are already providing links to more in-depth articles. --Bobthefish2 (talk) 17:38, 17 June 2011 (UTC)
replies: text: Hi Bobthefish2. I agree that we shouldn't describe individual methods in any detail otherwise the article will get very bloated. However, I think that it is important to mention BLAST specifically. This is another Top priority article in WikiProject Computational Biology and is perhaps the most influential peice of software in biology.  Its also a shame to remove the references for nedleman-wunsch and smith-waterman.  These are pretty important when considering sequence analysis.  In fact look at the text books such as Biological Sequence Analysis they are algorithm 101s.  Finally although I can cope with single and multiple sequence alignment being merged, there is a mix in the examples given.  For single sequence you now have algorithms, but for multiple alignment you have implemented software. So I think you should have say FASTA and BLAST as examples of pairwise sequence alignment.  I would then place the algorithms back in the context I had put them. Let me know what you think. I'm happy to make those changes if you are agreeable.  Thanks again for your help. Alexbateman (talk) 10:57, 18 June 2011 (UTC)
replies: text: I believe the pair-wise alignment algorithms are also published as tools, so they probably should be listed under pair-wise alignment. I have no experience with FASTA (other than the format!) but I am not very comfortable about listing BLAST because it's not really used for the same purpose as the likes of CLUSTAL, T-COFFEE, and such. It is, to me, more of a search tool. --Bobthefish2 (talk) 18:14, 22 June 2011 (UTC)
thread_title:  Methodology and Sequence Alignment sections 

message: The reference given for the first complete genome sequence is actually the second. The first complete genome sequence was bacteriophage MS2 published in 1976 (Nature 260 500 and earlier reports), which has RNA instead of DNA as its genetic material and was laboriously determined by classic RNA sequencing methods. (It should be noted that both the MS2 & the phiX174 sequence in ref. 7 were later revised.)
69.72.27.69 (talk) 22:50, 19 February 2013 (UTC)
thread_title:  First genome sequence