Archive for June, 2010

Plans for Rfam 2010-2011

June 30, 2010

Besides running RNA informatics courses Rfam peoples will be working on the usual summer family-building exercise together with a bright summer student. Priority number one will be building the published RNA Biology articles that we ran out of time to do for the Rfam 10.0 release:

SmY MRP Yfr2 tmRNA
Trypanosomal H/ACA ncRNAs GIR1 U3 SRP
influenza pseudoknot ptaRNA1 RsaOG rsmX

An exciting trend we’re starting to see is groups appending machine parsable alignments to their papers and writing Wikipedia articles for their families outside of the RNA families track. Of particular note are the 81 families from Zasha Weinberg’s latest papers [1-3] (see the table below). Also, Daniel Gautheret’s and Wade Winkler’s groups are supporting this effort with their respective CsfG RNA [4] and EAR motif [5] articles. Rightly or wrongly we are crediting some of this to the increased exposure of Rfam’s requirements from the RNA families track at the journal RNA Biology. This, by the way, for the first time has an impact factor, which is a fantastic 5.559. RNA Biology is punching well above its weight for now, long may this continue. Once our super summer student has finished with these (much easier families) he’ll be moving on to our terrifyingly long list of potential Rfam families that are waiting to be built. If you see anything on this list you might be interested in writing an RNA biology article for then please let us know as soon as possible.

In other news, we’re still hunting for good people to join a revamped Xfam group. In a few days we’ll be advertising Curator positions and we’re still looking for a Senior Computational Biologist. Check the Sanger Jobs site over the next few days.

[1] Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biology

[2] Weinberg Z, Perreault J, Meyer MM, Breaker RR (2009) Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature.

[3] Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. (2009) Identification of candidate structured RNAs in the marine organism ‘Candidatus Pelagibacter ubique’. BMC Genomics.

[4] Marchais A, Duperrier S, Gautheret D, Stragier P. (2010). A sporulation-specific, small noncoding RNA highly conserved in endospore formers. In preparation.

[5]  Irnov I & Winkler WC (2010) A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol.

6S-Flavo Acido-1 Acido-Lenti-1 Actino-pnp
AdoCbl-variant Bacillaceae-1 Bacillus-plasmid Bacteroid-trp
Bacteroidales-1 Bacteroides-1 C4-a1b1 C4
Chlorobi-1 Chlorobi-RRM Chloroflexi-1 Clostridiales-1
Collinsella-1 Cyano-1 Cyano-2 Dictyoglomi-1
Downstream-peptide Flavo-1 Gut-1 JUMPstart
L17DE Lacto-rpoB Lacto-usp Lnt
Methylobacterium-1 Moco-II Ocean-V Pedo-repair
PhotoRC-I PhotoRC-II Polynucleobacter-1 Pseudomon-1
Pseudomon-Rho Pseudomon-groES Pyrobac-1 Rhizobiales-2
SAM-Chlorobi SAM-I-IV-variant SAM-II_long_loops SAM-SAH
STAXI Termite-flg Termite-leu TwoGGAY
asd atoC crcB EAR
flg-Rhizobiales flpD gabT glnA
gyrA hopC lactis-plasmid leu-phe_leader
livK manA mraW msiK
nuoG pan pfl potC
psaA psbNH radC rmf
rne-II sbcD sucA-II sucC
traJ-II wcaG whalefall-1 yjdF
ykkC-III

Renaming of Transposases in Pfam

June 21, 2010

A few weeks ago the Pfam team was visited by the curators of the ISfinder resource, a specialist database that classifies eubacterial and archaeal transposases and insert sequences.  The ISfinder database has a very different role to Pfam: it focuses on this specific set of biological sequences and is the naming authority in the field for insertion sequences (ISs).  Pfam’s role is not to name transposases, but to identify the domains contained within these sequences.  Below we describe the outcomes of this meeting. Read the rest of this entry »

Xfam consortium meeting

June 4, 2010

The annual Xfam consortium meeting was held on the 10-11th May 2010 and we have the photographic evidence to prove it.

We spent the two days listening to talks from everyone about the latest developments.  We were particularly interested to hear about new developments in HMMER3 and INFERNAL – fundamental pieces of software that Xfam rely on.  Nucleotide enabled HMMER3 is in development and will be great for Rfam, hopefully replacing the current BLAST pre-filters.  We are also had updates on how the HMMER software scales using multiple threading and/or MPI.

We also had a number of wide ranging discussions.  Erik Sonnhammer unfortunately wasn’t present this time so the usual discussion on Stockholm alignment format was avoided.  However, we had a fulsome discussion of Pfam family naming nomenclature.  It was generally agreed that although there were rules followed for Pfam short names, no one else in the world understood them.  So we will endeavour to add a new section to our documentation about it.  We discussed how much information is actually required before a DUF (domain of unknown function) is renamed to something more meaningful.

We were blessed because the Icelandic ash cloud didn’t intervene.  But one of our number did leave their passport in a car bound for Oxford causing a delay home. We would like to thank all the members of the Pfam and Rfam consortia for coming and also to our other EBI attendees.

Janelia Farm Research Campus: Sean Eddy, Eric Nawrocki, Travis Wheeler, Tom Jones, Diana Kolbe, Michael Farrar

Stockholm Bioinformatics Center: Kristoffer Forslund, Dave Messina

Wellcome Trust Sanger Institute: Alex Bateman, Paul Gardner, Lars Barquist, Jaina Mistry, John Tate, Prasad Gunasekaran, Penny Coggill, Rob Finn

University of Manchester: Sam Griffiths-Jones

University of Oxford: Andreas Heger

University of Helsinki: Liisa Holm

Other friends from EBI: Sarah Hunter, Phil Jones, Craig McAnulla  and  Javier Herrero.

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