Monday, 29 April 2013

Second QSLiMFinder poster now on F1000 Posters

The second QSLiMFinder poster from the recent Cold Spring Harbor Laboratory "Systems Biology: Networks" meeting is now available at F1000 Posters:
  • Edwards RJ & Palopoli N. Computational prediction of short linear motifs mediating host-pathogen protein-protein interactions.
  • (I'm not sure why the last post about the other poster disappeared for a few days but it's back now!

    Thursday, 18 April 2013

    Latest QSLiMFinder poster now on F1000 Posters

    One of the QSLiMFinder posters from the recent Cold Spring Harbor Laboratory "Systems Biology: Networks" meeting is now available at F1000 Posters:
  • Palopoli N & Edwards RJ. Improved computational prediction of Short Linear Motifs using specific protein-protein interaction data.
  • With any luck, the other one will appear soon.

    Monday, 15 April 2013

    Second BUDAPEST paper published

    A second paper using BUDAPEST, "Responses of the Emiliania huxleyi proteome to ocean acidification" came out on Friday. An overview can be found in a University of Southampton press release, Marine algae show resilience to carbon dioxide emissions.
    A type of marine algae could become bigger as increasing carbon dioxide emissions are absorbed by the oceans, according to research led by scientists based at the National Oceanography Centre, Southampton (NOCS). The study, published this month in PLoS ONE, investigated how a strain of the coccolithophore Emiliania huxleyi might respond if all fossil fuels are burned by the year 2100 – predicted to drive up atmospheric CO2 levels to over four times the present day.
    You can read the rest of the press release here.

    There are some additional images and a video in a UC Santa Barbara press release, which gives a good summary of the science in the study.

    Bethan M. Jones, M. Debora Iglesias-Rodriguez, Paul J. Skipp, Richard J. Edwards, Mervyn J. Greaves, Jeremy R. Young, Henry Elderfield, C. David O’Connor (2013) Responses of the Emiliania huxleyi proteome to ocean acidification. PLoS ONE,

    Friday, 12 April 2013

    New Software Release

    New releases of SeqSuite, SLiMSuite and RJESuite are now available.

    Updates since last release:

    • budapest: Updated from Version 2.0.
    → Version 2.1: Improved handling of iTRAQ data using rje_mascot V1.2.

    • comparimotif_V3: Updated from Version 3.8.
    → Version 3.8: Changed scoring of overlapping ambiguities - uses IC of all possible ambiguities. Added "Ugly" match type.
    → Version 3.9: Added xgformat=T/F : Whether to use default CompariMotif formatting or leave blank for e.g. Cytoscape [True]

    • happi: Updated from Version 1.1.
    → Version 1.2: Added addclass and refined output for Host-Pathogen PPI analysis.

    • pingu: Updated from Version 3.7.
    → Version 3.8: Hopefully fixed issue of Fasta file generation log output writing to wrong log file.

    • qslimfinder: Updated from Version 1.4.
    → Version 1.4: Added qexact=T/F option for calculating Exact Query motif space (True) or estimating from dimers (False).
    → Version 1.5: Implemented SigV calculation. Modified extras setting.

    • seqmapper: Updated from Version 1.2.
    → Version 2.0: Reworked with new Object format, new BLAST(+) module and new seqlist module.

    • slimbench: Updated from Version 1.5.
    → Version 1.6: Added "simonly" to datatype - calculates both SN and FPR from "sim" data (ignores "ran") to check query bias.
    → Version 1.7: Added Benchmarking of ELM datasets without queries.
    → Version 1.8: Added Benchmarking dataset generation from PPI data and 3DID.

    • slimfinder: Updated from Version 4.4.
    → Version 4.5: Minor modifications to fix sigV and sigPrime bugs. Modified extras setting. Added palindrome setting for DNA motifs.

    • file_monster: Updated from Version 1.6.
    → Version 2.0: Major reworking with new object making use of rje_db tables etc. Old functions to be ported with time.

    • rje_dbase: Updated from Version 2.2.
    → Version 2.3: Added construction of EnsEMBL TaxaDB sets during TaxaDB construction.

    • rje_seqgen: Updated from Version 1.6.
    → Version 1.7: Modified/fixed ESTgen function to work for protein sequences.

    • ned_rankbydistribution: Updated from Version 1.0.

    • rje: Updated from Version 4.4.
    → Version 4.5: Modified randomString() and added stringShuffle() methods.

    • rje_blast_V1: Created.
    → Version 0.0: Initial Working Compilation.
    → Version 0.1: No Out Object in Objects
    → Version 1.0: Corrected to work with blastn (and blastp)
    → Version 1.1: Added special calling for Cerberus
    → Version 1.2: Added GABLAM and GABLAMO to BlastHit
    → Version 1.3: Added GABLAM calculation upon reading BLAST results and clearing Alignment sequences to save memory
    → Version 1.4: Tidied up the module with improved logging and progress reporting. Added dbCleanup.
    → Version 1.5: Added checking for multiple hits with same name and modified BLAST_Run.hitToSeq()
    → Version 1.6: Added nucleotide vs protein searches to GABLAM
    → Version 1.7: Added nucleotide vs nucleotide searches to GABLAM
    → Version 1.8: Added local alignment summary output to ReadBLAST()
    → Version 1.9: Added BLAST -C
    → Version 1.10: Added BLAST -g
    → Version 1.11: Added gablamfrag=X : Length of gaps between mapped residue for fragmenting local hits [100]
    → Version 1.12: Altered checkDB and cleanupDB to spot index files split over multiple files (*.00.p* etc.)
    → Version 1.13: Added localcut=X : Cut-off length for local alignments contributing to global GABLAM stats) [0]
    → Version 1.14: Added blast.checkProg(qtype,stype) to check whether blastp setting matches sequence formats.

    • rje_blast_V2: Created.
    → Version 2.0: Initial Compilation from rje_blast_V1 V1.14.

    • rje_db: Updated from Version 0.3.
    → Version 0.4: Improved use of AutoID and added Table.autoID() method.

    • rje_ensembl: Updated from Version 2.8.
    → Version 2.9: Reduced DNA chromosome downloads. Updated some species data. Added "known_by_projection" handling.

    • rje_genbank: Updated from Version 0.2.
    → Version 0.3: Added reloading of features.

    • rje_hmm_V1: Created.
    → Version 0.0: Initial Working Compilation.
    → Version 1.0: Working version with multiple HMM capacity
    → Version 1.1: Added hmmpfam option
    → Version 1.2: Cleaned up and debugged for rje_ensembl.ensDat()

    • rje_hmm_V2: Created.
    → Version 2.0: Initial HMMER3.0 version based on Version 1.2 and RJE_BLAST 2.0.

    • rje_markov: Updated from Version 2.1.

    • rje_mascot: Updated from Version 1.0.
    → Version 1.1: Fixed bugs for reading in data with unmatched peptides and iTRAQ data.
    → Version 1.2: Added

    • rje_menu: Updated from Version 0.2.
    → Version 0.3: Modified to work with new object types.

    • rje_ppi: Updated from Version 2.5.
    → Version 2.6: Added addPPI(hub,spoke,evidence) method. Added nodelist option.
    → Version 2.7: Added tabout=T/F Output PPI data as Node and Edge tables [False]

    • rje_seqlist: Updated from Version 1.1.
    → Version 1.2: Added seqshuffle option for randomising sequences.

    • rje_uniprot: Updated from Version 3.12.
    → Version 3.13: Minor bug fix for link table output.

    • rje_xref: Created.
    → Version 0.0: Initial Compilation.