Talk:Reviews:Directed evolution/Library construction

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General Comments

This is adapated more or less directly from the original text. The major modification is that Figure 2 has been removed as this was adapated from a paper in Nature Biotech. I could check up on the copyright issues but as this is a part of the review that needs modifications anyway I probably won't bother.

Todo List

Good place to list the things that need to be done on this review.

General presentation and logistics

References have been converted to biblio format. There is also now an Endnote style for generating a properly formatted text and reference list for biblio. The bibliography for the review has been placed on a separate page as I think this is probably the best way to do it as it will ultimately allow for linked bibliographies for a set of reviews in the area of directed evolution. The catch is that I've given them references that are just numbers (which correspond to record numbers in an Endnote file I have) so maintaining multiple bibliographies that are all cross compatible could get challenging.

Email appropriate editor at NAR to enquire about writing a short paper to get a primary citation for the WikiReview.

• Cameron Neylon 26 April 2007: Will wait on this until the review is more up to date before doing this.

Contact some directed evolution people to help out with curation.

• Cameron Neylon 26 April 2007: Done. Sent this email to people who cited the original review in papers describing new and improved methods for library construction.

It occurs to me it would be good to link the review to consensus protocols on OWW. Need to think about how to get a relatively large number of such protocols up on the system. If enough of the relevant people sign up as curators for the review then hopefully they can be persuaded to put up the relevant protocols as well.

Other issues?

Science and updating

Several areas need work to bring this up to date. If anyone has some particular references that they feel should be included it would be helpful to categorise them below. General criteria is that they need to give a good description of the methodology and any practical issues as well as apply it to a real experiment.

In vivo error prone methods

http://aem.asm.org/cgi/content/full/67/8/3645?view=long&pmid=11472942

Error-prone PCR methods

http://dx.doi.org/10.1016/j.ab.2004.11.032

pmid=15585138 - this link seems to be broken, currently checking

http://journals.humanapress.com/index.php?option=com_opbookdetails&task=articledetails&category=humanajournals&article_code=ABAB:117:2:115

http://nar.oxfordjournals.org/cgi/content/full/32/22/e176

http://www.biomedcentral.com/1472-6750/7/18

http://dx.doi.org/10.1016/j.jbiotec.2004.10.016 - this may belong in RID methods below

http://www.nature.com/nbt/journal/v22/n6/abs/nbt974.html

http://nar.oxfordjournals.org/cgi/content/full/32/19/e145

http://dx.doi.org/10.1016/j.bioeng.2004.10.004

http://pubs.acs.org/cgi-bin/article.cgi/bipret/2004/20/i06/html/bp049925z.html - generation of random sequences

http://www.nature.com/nprot/journal/v1/n5/abs/nprot.2006.403.html - protocol for whole plasmid error prone RCA

Random insertion/deletion methods

Quite a lot to be done here. Need a new picture for this class.

http://nar.oxfordjournals.org/cgi/content/full/33/9/e80

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16493137 - I guess this belongs here

http://nar.oxfordjournals.org/cgi/content/full/32/3/e26

Directed methods

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17446890&query_hl=4&itool=pubmed_docsum

http://www.biomedcentral.com/1472-6750/4/2

http://nar.oxfordjournals.org/cgi/content/full/32/14/e115

http://jbt.abrf.org/cgi/content/full/18/3/147

http://dx.doi.org/10.1016/j.ab.2003.10.012

http://ajpcell.physiology.org/cgi/content/full/288/6/C1273

http://nar.oxfordjournals.org/cgi/content/full/30/16/e84

Recombination methods

http://nar.oxfordjournals.org/cgi/content/full/33/13/e117

http://www.nature.com/nbt/journal/v20/n10/abs/nbt736.html

http://nar.oxfordjournals.org/cgi/content/full/29/20/e97

http://www3.interscience.wiley.com/cgi-bin/abstract/110489948/ABSTRACT

http://aem.asm.org/cgi/content/full/68/12/6146?view=long&pmid=12450839

http://nar.oxfordjournals.org/cgi/content/full/33/9/e82

http://www.nature.com/nprot/journal/v1/n4/abs/nprot.2006.309.html - protocol on Nature Protocols

• Cameron Neylon 17 July 2007: I've added a bunch of things here as I came across them while looking for ep-PCR related papers.

Other tools

http://bioinformatics.oxfordjournals.org/cgi/content/full/21/15/3314

http://dx.doi.org/10.1006/jtbi.2000.2082

Analysis of mutation methods

There is now a significant amount of work on analysis, both functional and theoretical of mutations methods and how this relates to results of the DE experiment. Perhaps a new section is required to cover this?

http://www.blackwell-synergy.com/doi/abs/10.1046/j.1462-2920.2002.00326.x

http://dx.doi.org/10.1016/j.jmb.2005.05.023

http://nar.oxfordjournals.org/cgi/content/full/33/11/3667

http://www.liebertonline.com/doi/abs/10.1089%2F10665270050081423

http://peds.oxfordjournals.org/cgi/content/full/16/6/451

http://peds.oxfordjournals.org/cgi/content/full/19/6/245 (?)

http://www.pnas.org/cgi/content/full/101/25/9205

http://dx.doi.org/10.1016/j.bioeng.2005.06.001

http://dx.doi.org/10.1016/j.jmb.2005.10.082