Talk:Chromosome walking
The article makes a basic mistake, I think: If you are chromosome walking, you are not necessarily sequencing. e.g. You might be mapping. And while you might walk by sequencing minimally the ends of each fragments, I think you could walk just by detecting hybridization and without ever learning the sequence of the overlapping regions. I suspect the technique predates sequencing altogether. 168...
- Chromosome walking was first described in the paper that mapped the CFTR gene (Cystic Fibrosis)... 1988 or so, IIRC. I'll see if I can dig up the reference, and I think it did not involve sequencing. I think this method is also called "primer walking", when it is done in the manner described in the article. I'll have to double check that also. AdamRetchless 01:22, 23 Mar 2005 (UTC)
Here's the paper's abstract [1]. I'm pretty sure that it is the first instance of chromosome walking. Based upon my literature search, it looked like the idea of reverse genetics was also developed in the context of the search for the CF gene. AdamRetchless
- That paper isn't the first use of chromosome walking (it refers to "conventional chromosome walking methods". I also agree with 168...; chromosome walking is really the identification of an overlapping set of subclones. What this article talks about is "primer walking" (or perhaps "sequence walking". And I have issues with the sentence "The method can be used to sequence entire chromosomes (thus, chromosome walking)." Although in theory it could, in practice primer walking from one end to the other would take too long. Even subcloning regions and sequencing them in parallel, it took the human genome project thousands of people several years to do the bulk of it. And getting a good read off genomic DNA is very difficult.
So I think the text of this article should be moved to primer walking, (currently a stub), and a new article started to describe true chromosome walking. Loris 20:10, 27 July 2005 (UTC) - In my opion, chromosome walking start by screening BAC /YAC library with flaking molecular markers (that you obtained from map-based, transcription-based or even silicol-based approaches), after sequence whole single clone, you have to develop new molecular marker from this sequence and check it on mapping population to make sure you are in right direction. Furthermore, one repeat screen library (overlapping set of subclones) until having full length contig. Vietbio 23:53, 29 August 2005 (UTC)
- That paper isn't the first use of chromosome walking (it refers to "conventional chromosome walking methods". I also agree with 168...; chromosome walking is really the identification of an overlapping set of subclones. What this article talks about is "primer walking" (or perhaps "sequence walking". And I have issues with the sentence "The method can be used to sequence entire chromosomes (thus, chromosome walking)." Although in theory it could, in practice primer walking from one end to the other would take too long. Even subcloning regions and sequencing them in parallel, it took the human genome project thousands of people several years to do the bulk of it. And getting a good read off genomic DNA is very difficult.
So how do you do the sequencing then?
[edit]There's something odd about this article: Sequencing lists this as a method used to sequence DNA, but this article says "2. The new short DNA strand is sequenced." How can the second step of sequencing be sequencing? Does it mean, "...is sequenced using sequencing method X"? Of the three methods mentioned under sequencing, only Chain termination method seems to actually be a method of sequencing, the other two just refer back to some unexplained "sequencing" process. Anyone care to clarify? - IMSoP 00:19, 22 Oct 2004 (UTC)
- Fixed (I hope I got it right). - IMSoP 21:17, 14 Nov 2004 (UTC)
- The issue arises because what biologists want is to get a full length sequence, and call that entire process "sequencing". But practically only a short region can be determined at a time - and this step is also called "sequencing". Both are quite reasonable, I think. To avoid confusion, I suggest calling the former a "sequencing strategy". Loris 20:10, 27 July 2005 (UTC)
Primer Walking is a better term.
[edit]Chromosome walking is a term that pretty obviously originated in genomics. The trick is that the same process is used in metagenomics as well where the sample contains DNA isolated from an entire community. Most metagenomic sequencing efforts pull out low coverage fragments of genomes (usually of bacteria or viruses) from the community which can then be primer walked to get the whole genome if a particular fragment is intriguing. In the long run there's way more sequence content (due to really high diversity when you get to those scales) that's likely to be generated by these methods making "chromosome walking" a name that's likely to look pretty archaic in the coming years. - JenniferForUnity 03:12, 6 December 2006 (UTC)