Posts Tagged ‘pfam’

Pfam 30.0 is available

July 1, 2016

Pfam 30.0, our second release based on UniProt reference proteomes, is now available. The new release contains a total of 16,306 families, with 22 new families and 11 families killed since the last release. The UniProt reference proteome set has expanded and now includes 17.7 million sequences, compared with 11.9 million when we made Pfam 29.0. In this release, we have updated the annotations on hundreds of Pfam entries, and renamed some of our Domains of Unknown Function (DUF) families.

DUFs are protein domains whose function is uncharacterised. Over time, as scientific knowledge increases and new data about proteins comes to light, more information about the function of a domain may become available. As a result, DUFs can be renamed and re-annotated with more meaningful descriptions. As part of Pfam 30.0, we have re-annotated 116 DUFs based on updated information in the UniProtKB database, the scientific literature, and feedback from Pfam and InterPro users. Examples of some our DUF updates in Pfam 30.0 are given below:

 

  • PF10265, created in release 23.0 and originally named DUF2217, has been renamed to Miga, a family of proteins that promote mitochondrial fusion.
  • PF10229, created in release 23.0 and originally named DUF2246, has been renamed as MMADHC, as it represents methylmalonic aciduria and homocystinuria type D proteins and their homologues.  The structure of this domain is shown below.

 

5cv0

Structure of MMADHC dimer, PDB:5CV0

 

  • PF12822, created in release 25.0 and originally named DUF3816, has been renamed to ECF_trnsprt, since it contains proteins identified as the substrate-specific component of energy-coupling factor (ECF) transporters.

Please note that we may change the identifier for a family (e.g. DUF2217), but we never change the accession for a family (e.g. PF10265).

If you find any more DUFs that can be assigned a name based on function, or any other annotation updates, please get in touch with us (pfam-help@ebi.ac.uk).

 

Pfam 29.0 is now available

December 22, 2015

Pfam 29.0, our second release of 2015, contains 16295 entries and 559 clans. We have made some major changes to our underlying sequence database and the data that are displayed on the website, which we’ve outlined below. Full details can be found in our Nucleic Acids Research paper, which is available here. Read the rest of this entry »

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)

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