Talk:Sequence analysis

Untitled

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)

Methodology and Sequence Alignment sections

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)

Hi Bobthefish2,

I'd like to help out improving this article. I intend to add new sections on various important topics in the field:

• history
• structure prediction
• domain hunting (possibly)
• gene prediction
• etc, etc

I wouldn't agree with having long lists of software on these pages, but we should certainly add links to the relevant list articles such as List of phylogenetics software and List of alignment visualization software. Alexbateman (talk) 12:03, 17 June 2011 (UTC)

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)

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)

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)

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)

First genome sequence

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)

• I assume you are referring to this paper: Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M (8 Apr 1976). "Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene". Nature. 260 (5551). doi:10.1038/260500a0. PMID 1264203. {{cite journal}}: Unknown parameter |paages= ignored (help)CS1 maint: multiple names: authors list (link) If so, can you provide a source claiming this as the "first complete genome sequence"? --Thorwald (talk) 23:17, 19 February 2013 (UTC)

     From the opening paragraph of that paper: "As the sequences for the other regions of this RNA have been
     published already, the complete, primary chemical structure of a viral genome has now been established."
     69.72.27.69 (talk) 03:26, 20 February 2013 (UTC)
     Also, from the Wikipedia entry Bacteriophage MS2: "In 1976, the MS2 genome was the first genome to be
     completely sequenced." (cites above paper)
     69.72.27.161 (talk) 23:34, 21 February 2013 (UTC)