SIBsim4 / News: Recent posts

SIBsim4 version 0.20 is released

SIBsim4 is a tool to align transcribed RNA sequences on a genomic DNA template.

This release introduces a new command line switch -S which allows to better fine tune how insertions/deletions are evaluated around potential splice junctions. A few problems where spurious very small exons or large gaps in exons were incorrectly reported have been fixed. The code was cleaned up to silence new warnings from the current GCC releases.

Posted by Christian Iseli 2010-04-19

SIBsim4 version 0.17 is released

SIBsim4 is a tool to align transcribed RNA sequences on a genomic DNA template.

This release introduces a chimera detection feature in SIBsim4.

Posted by Christian Iseli 2008-05-06

SIBsim4 version 0.16 is released

SIBsim4 is a tool to align transcribed RNA sequences on a genomic DNA template.

This release fixes excessive run-time in some cases of partially repeated sequences.

All users are encouraged to update.

Posted by Christian Iseli 2007-12-01

SIBsim4 version 0.15 is released

SIBsim4 is a tool to align transcribed RNA sequences on a genomic DNA template.

This release add a -s option to control how potential duplicated genes are detected, instead of abusing the -f option.

Posted by Christian Iseli 2007-04-24

SIBsim4 version 0.14 is released

This version introduces two new options, -c and -f,
providing full control over how results are filtered.

This allows better detection of duplicated genes,
where duplicates are not complete or well preserved.

Posted by Christian Iseli 2006-11-13

SIBsim4 version 0.13 is released

SIBsim4 is a tool to align expressed RNA sequences on a DNA template.

This update fixes some failures in detecting duplicated genes.

Another change is to obey the default value of the K and C parameters instead of trying to compute them on the fly.

The last change avoids dependancy on the math library.

Posted by Christian Iseli 2006-06-19

SIBsim4 version 0.12 is released

Version 0.12 of SIBsim4 has been released.

This version fixes a bug where a spurious polyA tail was wrongly detected in some cases. The consequence was a failure to detect some exons in the affected transcripts.

This version also introduces a warning to the user when multiple sequences are detected in the DNA file.

Posted by Christian Iseli 2006-06-09

SIBsim4 version 0.11 is released

This is a bugfix release, to fix a bug in the -o switch. The bug caused the output DNA sequence header to be inaccurate.

Posted by Christian Iseli 2006-03-09

SIBsim4 version 0.10 is released

This is a bugfix release, to fix a bug in the -o switch. The bug caused the output DNA coordinate to be wrong on exons end-points.

Posted by Christian Iseli 2006-02-21

SIBsim4 version 0.9 is released

Version 0.9 of SIBsim4 has been released.

This new version avoids the creation of spurious very small exons.

A new -o switch has been added to enable the specification of the overall position of the DNA sequence on the global chromosome coordinates.

There also is the usual assortment of bug fixes and code cleanup.

See http://sibsim4.sf.net for full details.

Posted by Christian Iseli 2006-01-16

SIBsim4 version 0.8 available

SIBsim4 is a similarity-based tool for aligning a collection of expressed sequences (EST, mRNA) with a genomic DNA sequence.

This version improves splicing and fixes a few bugs.

http://sibsim4.sourceforge.net

Posted by Christian Iseli 2004-08-27

SIBsim4 version 0.7 is now available

SIBsim4 is a similarity-based tool for aligning a collection of expressed sequences (EST, mRNA) with a genomic DNA sequence.

This version improves splicing and polyA handling.

Posted by Christian Iseli 2004-06-23

New SIBsim4 version available

A new release of SIBsim4 is now available.

SIBsim4 is a similarity-based tool for aligning a collection of expressed sequences (EST, mRNA) with a genomic DNA sequence.

Please check its homepage for further details: http://sibsim4.sourceforge.net

Posted by Christian Iseli 2004-05-27

Initial release

The initial public release of SIBsim4 is now available.

SIBsim4 is a similarity-based tool for aligning a collection of expressed sequences (EST, mRNA) with a genomic DNA sequence.

Please check its homepage for further details: http://sibsim4.sourceforge.net

Posted by Christian Iseli 2004-04-30