Posts Tagged ‘pfam’

Moving to xfam.org

May 1, 2014

Back in November 2012 we announced that the Xfam team in the UK was moving from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute (EMBL-EBI), just next door on the Wellcome Trust Genome Campus. On Tuesday we completed that move by switching off the Pfam and Rfam websites inside Sanger and redirecting all traffic to our shiny new home at xfam.org. You can now find the Pfam and Rfam websites at pfam.xfam.org and rfam.xfam.org respectively. Read the rest of this entry »

Short-term Pfam position available.

February 7, 2014

We have just advertised a 9-month maternity cover position in Pfam. We are looking for a skilled Bioinformatician to help us take Pfam into its next phase of development as we become more integrated into the European Bioinformatics Institute (EMBL-EBI).

Essential knowledge, skills and experience:

  • Degree in Science with relevant experience
  • Computer literacy (unix experience)
  • Programming skills in Perl, including OO Perl
  • Familiarity with writing production software
  • MySQL, or similar, expertise
  • Experience working with biological sequence data
  • Good communications skills

See all the details on the EBI jobs page.

Join Rfam, see the world

January 31, 2014

Rfam is recruiting! We are currently recruiting an RNA informatician to join our team. We’re looking for someone really enthusiastic about RNA and who’s interested in working with Rfam as we move to genome-based alignments and explore new technologies for the database and website.

If this is you, why not apply to join us as a Senior Bioinformatician?

We’ve moved, now the websites

January 30, 2014

In November 2012, we announced that the Xfam groups were moving the few tens of metres from the Wellcome Trust Sanger Institute to the European Bioinformatics Institute. We warned you then, that the websites would also eventually move. Read the rest of this entry »

A version of pfam_scan.pl for HMMER 3.1b

October 15, 2013

We’ve had a lot of questions from users recently, wondering why our pfam_scan.pl script doesn’t work with the latest release of the HMMER package, version 3.1b. This is a quick post to explain why that is, and what we’ve done about it. Read the rest of this entry »

Case studies from the list of human regions not in Pfam 27.0.

May 14, 2013

Following on from Jaina and Marco’s blog post last week about conserved Human regions not in Pfam, I would like to give you some examples of how we have used the regions identified to improve existing Pfam families, and to create new ones. When available, we use three-dimensional structures to guide the boundary definitions of our families. In cases where there is no available structure, either for the protein in question or for other proteins in the same Pfam family, we base boundary decisions on sequence conservation. The following paragraphs give three examples of cases I have looked at recently.

Read the rest of this entry »

Pfam targets conserved human regions

May 7, 2013

Recently, we have been looking at how much of the human proteome is covered by Pfam (release 27.0), and ways in which we can improve this coverage. We have even written an open access paper about it that you can read here [1]  that is part of the proceedings of the 2013 Biocuration conference. We used the human proteins in UniProtKB/Swiss-Prot [2] (~20,000 sequences) as our human proteome set, and found that while most of the sequences in this set have some Pfam annotation (90% have at least one Pfam domain), there is still much ground to cover before we have a complete map of all (conserved) human regions (HRs). Here, rather than repeating what we presented in the paper (did we mention it is open access? :-)), we would like to tell you more about the impact this study is having on our strategies for selecting target regions to be added to Pfam.

Read the rest of this entry »

TreeFam 9 is now available!

May 3, 2013

We are happy to announce that TreeFam 9 is online and you can find it under http://www.treefam.org.

TreeFam 9 now has 109 species (vs. 79 in TreeFam 8) and is based on data from Ensembl v69, Ensembl Genomes v16, Wormbase and JGI.

This release marks an important step for TreeFam as it is the first release build since TreeFam has been resurrected.
Here is a list of the most important changes in TreeFam 9:

  • New website layout (adopting the Pfam/Rfam/Dfam layout)
  • Infrastructure move of web servers and databases to the EBI
  • Sequence search against the library of TreeFam family profiles
  • new tree visualisations in pure javascript using D3, e.g. see the BRCA2 gene tree here.
  • Pairwise homology download

We hope you find all the information you are looking for. If you don’t, please let us know so that we can include the information you want. The old website will remain online here.

If you have questions, suggestions or find bugs, don’t hesitate to contact us through our new forum here.

Happy treefamming,

the TreeFam team
(Fabian, Mateus)

Pfam 27.0 is now available!

March 22, 2013

In a blog post published just over a year ago, I proposed a number of changes to the content of Pfam to improve scalability and usability of the database.  These changes came into effect a few days ago, when we released Pfam 27.0.  This release of Pfam contains a total of 14831 families, with 1182 new families and 22 families killed since release 26.0. 80% of all proteins in UniProt contain a match to at least one Pfam domain, and 58% of all residues in the sequence database fall within a Pfam domain. Read the rest of this entry »

Dfam 1.1 released

November 15, 2012

We are pleased to announce that we’ve released Dfam 1.1. This version represents a few important changes from 1.0, including updated hit results, a new tab for each entry page showing relationships to other entries, and improved handling of redundant profile hits.

Read the rest of this entry »

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