July 2008 - beg-evodevo@psb.ugent.be

[Beg-evodevo] NRG :: Horizontal gene transfer in eukaryotic evolution
by Klaas Vandepoele 29 Jul '08

29 Jul '08

Horizontal gene transfer in eukaryotic evolution Patrick J. Keeling^1 <http://www.nature.com/nrg/journal/v9/n8/full/nrg2386.html#a1> & Jeffrey D. Palmer^2 <http://www.nature.com/nrg/journal/v9/n8/full/nrg2386.html#a2> <http://www.nature.com/nrg/journal/v9/n8/authors/nrg2386.html> -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-evodevo] Comparative genomics: Lining up is hard to do
by Klaas Vandepoele 20 Jul '08

20 Jul '08

http://www.nature.com/nrg/journal/v9/n8/full/nrg2420.html Fulltext: Nature Reviews Genetics 9, 573 (August 2008) | doi:10.1038/nrg2420 Comparative genomics: Lining up is hard to do Tanita Casci Comparisons between proteins or between DNA stretches tell a story about the evolutionary past. Unfortunately, however, which story they tell often depends on which method is used to line up the sequences. A new method claims to improve the accuracy of current alignments by making use not only of the similarity between sequences but also their phylogenetic history. Commonly used methods for aligning multiple sequences rely on sequential pairwise alignments between sequences --- the most closely related sequences are aligned first, followed by progressively more distant ones, all the way down the evolutionary tree. The problem with these so-called 'progressive algorithms' is that it is impossible to distinguish insertions from deletions when using only two sequences, causing biases that distort subsequent alignments. Traditional implementations of this algorithm set a higher penalty for insertions than for deletions and deem the former less likely to have occurred. These biases are particularly problematic when there are multiple neighbouring insertions or deletions --- for example, such insertions end up being aligned one under the other even though, by definition, they are not evolutionarily related. Misleading alignments caused by these false homologies are propagated, and lead to incorrect inferences about sequence evolution. Two sequences do not contain information about whether a length difference between them is caused by an insertion or a deletion --- however, in a multiple (as opposed to pairwise) alignment there are more than two sequences. The new phylogeny-aware algorithm uses outgroup information from related sequences to infer which of the two possible changes has happened. It does so by 'flagging' the gaps (length changes) made in earlier alignments so that they can be accounted for in future alignments without incurring a penalty. The re-use of a flagged gap also indicates that a particular length change was created by an insertion; the gap can then be labelled as a 'permanent' insertion and correctly kept distinct from any neighbouring ones. The new algorithm, called PRANK <http://www.ebi.ac.uk/goldman-srv/prank/>, was tested on simulated sequence data. Traditional methods were shown to introduce biases, and therefore misalignments, even when sequences are closely related. PRANK performs better than traditional methods in this situation and shows no bias as the sequences get more diverged and become harder to align. It is striking that traditional methods are error prone even when sequences get increasingly similar --- indicating that denser species sampling and more DNA sequencing cannot correct the algorithmic flaw in the alignment. Correct alignment remains a challenge, but less so than in the past. Why have programs traditionally performed so badly? The authors suggest that alignments were historically developed to compare protein sequences, in which any biases would be likely to cluster harmlessly in unconstrained regions. Given the increasingly widespread analysis of genomic DNA for understanding evolution there is a pressing need to get these methods up to scratch. Links WEB SITE * PRANK <http://www.ebi.ac.uk/goldman-srv/prank> Top of page <http://www.nature.com/nrg/journal/v9/n8/full/nrg2420.html#top> References and links ORIGINAL RESEARCH PAPER 1. Löytynoja, A & Goldman, N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320, 1632--1635 (2008) * Article <http://dx.doi.org/10.1126/science.1158395> * PubMed <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=P…> * ChemPort <http://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg…> FURTHER READING

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[Beg-evodevo] Interacting Gene Clusters and the Evolution of the Vertebrate Immune System -- Makino and McLysaght, 10.1093/molbev/msn137 -- Molecular Biology and Evolution
by Klaas Vandepoele 08 Jul '08

08 Jul '08

http://mbe.oxfordjournals.org/cgi/content/abstract/msn137v1?ijkey=ZzMlJ7fho… -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-evodevo] new shares transreg and evodevo
by Klaas Vandepoele 07 Jul '08

07 Jul '08

Dear evodevo / transreg people, as you might know IT is planning to separate all BEG data over multiple shares in order to allow better quota management & future enlargements of disk sizes. The goal is to free some space from /group/biocomp/users/ and /group/biocomp/projects/ by moving data to (or starting new projects in) /group/biocomp/evodevo/ or /group/biocomp/transreg/. These two folders are (getting) synchronized so that in the near future (~2 weeks) they will become new shares (like has already been done for annotation and sysbiol). So if possible please archive your old data and move current projects to these two new folders and in the near future you will have access to new shares with more free disk space. thanks & best regards, Eric, Luc & Klaas FYI: Current contents */group/biocomp/transreg/* drwxr-xr-x 6 elwis biocomp 4.0K Jun 10 11:17 elwis drwxr-xr-x 10 klpoe biocomp 4.0K Jun 30 11:56 klpoe drwxrwxrwx 5 samov biocomp 4.0K Apr 17 12:04 samov Current contents */group/biocomp/evodevo/* drwxrwx--- 5 stbod biocomp 4.0K Dec 13 2007 projects with inside projects/ drwx------ 6 root root 4.0K Jan 17 14:44 PLAZA* drwxrwx--- 3 yvsae biocomp 8.0K Feb 8 14:36 ppi_stefanie drwxr-xr-x 5 tiblo biocomp 8.0K May 29 11:17 tiblo * note that the PLAZA folder is already closed. The new share is /group/plaza/ drwxrwx--- 7 stbod biocomp 4.0K May 27 13:16 users with inside users/ drwxrwx--- 13 sepro biocomp 4.0K Jul 4 13:09 sepro drwxrwxrwx 4 sepro biocomp 4.0K Jun 19 15:02 sepro_pub drwxrwx--- 57 stbod biocomp 8.0K Jul 4 14:40 stbod drwxrwx--- 5 tiblo biocomp 4.0K May 23 11:16 synteny drwxr-xr-x 7 tiblo biocomp 4.0K Jun 20 13:41 tiblo */group/plaza/* drwxrwxr-x 8 klpoe biocomp 4.0K May 28 14:21 data drwxr-xr-x 5 kebil biocomp 4.0K Sep 27 2007 lib drwxr-xr-x 4 kebil biocomp 4.0K Sep 27 2007 old_lib -rwxr-xr-x 1 kebil biocomp 368 Sep 27 2007 README drwxrwxr-x 8 kebil biocomp 4.0K Oct 8 2007 sandbox -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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