Bioinformatics @ bugaco.com

Website to convert sequences

Thursday, August 20, 2009 @ 12:08 am

New website that converts sequences is available. It supports 17 commonly used sequence formats.

StarORF available at MIT STAR site

Friday, March 13, 2009 @ 9:44 am

There is interesting software for looking at Open Reading Frames at MIT STAR site. It allows you to paste sequence, do reverse complement and search for ORFs in the sequence.

Thursday, August 2, 2007 @ 3:56 pm

Gontang, Fenical and Jensen used Clusterer to analyse data in manuscript Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments.

ClustalW documentation accessable online

Saturday, December 9, 2006 @ 10:27 pm

Documentation for ClustalW, a general purpose multiple alignment program for DNA or proteins, is posted on Bugaco .com bioinformatic's documentation section.

New Online Nexus to Mega converter

Friday, January 6, 2006 @ 2:46 pm

New Nexus to Mega converter is available at Bugaco's bioinf section. Tools allows user to copy/paste data to online form and perform easy conversion from Nexus to Mega format.

Online Nexus to Fasta converter

Friday, January 6, 2006 @ 2:42 pm

New Nexus to Fasta converter is available at Bugaco's bioinf section. Tools allows user to copy/paste data to online form and perform easy conversion from Nexus to FASTA format.

Klepac-Ceraj V, Ceraj I, Polz MF Clusterer: extendable java application for sequence grouping and cluster analyses, Online Journal of Bioinformatics, 7 (1) : 15-21, 2006

Sunday, December 18, 2005 @ 2:51 pm

Clusterer manuscript has been published at: Klepac-Ceraj V, Ceraj I, Polz MF Clusterer: extendable java application for sequence grouping and cluster analyses, Online Journal of Bioinformatics, 7 (1) : 15-21, 2006.
Clusterer is available at Polz website

Clusterer supports NEXUS and FASTA

Sunday, May 9, 2004 @ 9:29 pm

Clusterer now supports NEXUS and FASTA as input file formats. Clusterer supported FASTA format from its inception, NEXUS format is more complex and due to development constrains was not added to initial release.
NEXUS file format is added to the Clusterer to help its faster adoption.

Chimera Buster is acknowledged in journal of Environmental Microbiology

Thursday, May 6, 2004 @ 4:47 am

Chimera Buster, novel algorithm for finding putative chimerical sequences in clone libraries with high coverage is acknowledged in Vanja�s article. Article appeared in Environmental Microbiology under title "High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria".

Quote from the article: �The data were also checked for putative chimeras by the RDP Chimera_Check (Maidak et al., 1999) and the ChimeraBuster algorithm, which was newly developed to specifically analyze clone libraries with high coverage.�

Clusterer issues with Java 2 v1.3 discovered

Wednesday, February 11, 2004 @ 11:14 pm

I discovered today some issues with Java 2 v1.3. They are related to Swing (User Interface) methods new to JDK 1.4.
Please use Java 2 v1.4 until this issues are resolved.
"Open local file" feature is added, to make it easier to paste fasta file into Clusterer.
Thanks,
Ivan

Bioinf @ bugaco is undergoing facelifting

ivan@bugaco.com — Sunday, February 1, 2004 @ 4:51 am

New design and layout of bioinformatics @ bugaco.com is underway. New look & feel should allow easier and clearer navigation on the site.
Most of the redesign should be done by mid February.

Preview of 'Linebreaker Applet'

Saturday, January 3, 2004 @ 5:00 am

Linebreaker applet is new applet posted on bioinformatics @ bugaco. Tool provides an UI for conversion between line break formats used by UNIX, Machintosh and Windows. To start this tool use click here. This tool will get its place on menu bar soon.

Blog added to bioinf section of bugaco.com

Saturday, December 27, 2003 @ 9:58 pm

Dear Visitor,
Blog is added to bioinformatics @ bugaco.com to help better understand user community, to get feedback about tools, and to get fresh ideas how to improve user experience with tools provided.