[X] The "/OldFiles" file could not be found or is not available. Please select another file.

ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.


http://aspipe.sourceforge.net





Separate each tag with a space.

Release Date:

2008-10-17

Topic:

Operating System:

License:

Intended Audience:

Database Environment:

Programming Language:

Registered:

2007-01-08

Ratings and Reviews

Be the first to post a text review of ASpipe. Rate and review a project by clicking thumbs up or thumbs down in the right column.

Project Feed

  • File released: /aspipe/ASpipe2.1.5/ASpipe2.1.5.tar.gz

    posted 447 days ago

  • aspipe ASpipe2.1.5 file released: ASpipe2.1.5.tar.gz

    Version 2.1.5 Updated: Oct 17, 2008 Add "commit" to some insert syntax. As discovered on some machine, the insertion was done in buffer, another process started before the autocommit, which will cause wrong eTranscript prediction. Version 1.9 Updated: May 21 2008 (1) library/AS.pl: Fixed a bug in AS.pl where some IntronR events was predicted wrong (2) library/MergeExon.pl Consider fuzzy border option, some terminal exons may have splicing site not predicted well (3) library/cluster.pl Restructure the algorithm of clustering EST alignments, merge single exon with its neighboring clusters. (4) library/GetDBSeq.pl, bin/ASpipe.pl Add a new 'Hybrid' method of retrieving genome sequences, requires fastacmd and formated genomic database. Reduced memory usage. (5) bin/ASIPtoGFF3.pl Assign ? as the orientation to single exon Version 1.8 Updated: May 15 2008 (1) Fixed known bugs as of May 15 2008 (2) Cross-species EST model incoporated (3) Read input from GFF format file (4) Output in GFF format file

    posted 447 days ago

  • New version of ASpipe released

    A stable version of ASpipe (ASpipe2.1.5) is now available at SourceForge. The new version fixed previous minor bugs and added some new features including output in GFF format. An perl-cgi based browser (ASviewer) to visualize the ASpipe data is available upon request. Please cite the following paper if you are using ASpipe: (1) Wang, B.-B., O'Toole, M., Brendel, V. & Young, N.D (2008) BMC Plant Biology Cross-Species EST Alignments Reveal Novel and Conserved Alternative Splicing Events in Legumes (2) Wang, B.-B. and Brendel, V. (2006) PNAS Genome-wide comparative analysis of alternative splicing in plants

    posted by bingbingwang 455 days ago

  • File released: /aspipe/ASpipe1.0.1/ASpipe1.0.1.tar.gz

    posted 969 days ago

  • aspipe ASpipe1.0.1 file released: ASpipe1.0.1.tar.gz

    Version 1.0.1 1/26/2007 (1) Updated ASpipe.pl, now write some important parameters to the log. (2) Updated GMAP_extract.pl, Fixed GMAP orientation confusion problem by reverse the genome strand when cDNA is antisense. See details in the script.

    posted 969 days ago

  • Code committed

    Anonymous committed patchset 1 of module CVSROOT to the ASpipe CVS repository, changing 11 files

    posted by nobody 1095 days ago

  • Project Information Updated

    bingbingwang registered the ASpipe project

    posted by bingbingwang 1095 days ago

  • Forum thread added

    Anonymous created the Welcome to Developers forum thread

    posted by nobody 1095 days ago

  • Forum thread added

    Anonymous created the Welcome to Help forum thread

    posted by nobody 1095 days ago

  • Forum thread added

    Anonymous created the Welcome to Open Discussion forum thread

    posted by nobody 1095 days ago

Rate and Review

Be the first person to add a text review.

Would you recommend this project?






<

Related Projects

Thanks for your rating!

Would you also like to write a review?





Skip Review

Thanks for your review!

Get credit for your review by logging in via OpenID. Click your account provider:

No Thanks