Virology and Bioinformatics from Virology.ca
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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Sequenceserver: a modern graphical user interface for custom BLAST databases « Homolog.us – Bioinformatics

Abstract: The dramatic drop in DNA sequencing costs has created many opportunities for novel biological research. These opportunities largely rest upon the ability to effectively compare newly obtained and previously known sequences. This is commonly done with BLAST, yet using BLAST directly on new datasets requires substantial technical skills or helpful colleagues. Furthermore, graphical interfaces for BLAST are challenging to install and largely mimic underlying computational processes rather than work patterns of researchers. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver (http://sequenceserver.com), a modern graphical user interface for BLAST. Sequenceserver substantially increases the efficiency of researchers working with sequence data. This is due first to innovations at three levels. First, our software can be installed and used on custom datasets extremely rapidly for personal and shared applications. Second, based on analysis of user input and simple algorithms, Sequenceserver reduces the amount of decisions the user must make, provides interactive visual feedback, and prevents common potential errors that would otherwise cause erroneous results. Finally, Sequenceserver provides multiple highly visual and text-based output options that mirror the requirements and work patterns of researchers. Together, these features greatly facilitate BLAST analysis and interpretation and thus substantially enhance researcher productivity.

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BLASTing Off – How BLAST Works

BLASTing Off – How BLAST Works | Virology and Bioinformatics from Virology.ca | Scoop.it
More than a pun on the explosive growth of sequencing data, BLAST makes annotation and comparisons of similar sequences much easier. Created by a group at the U.S. National Center for Biotechnology Information in…
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iPhylo: BLAST a sequence and get a tree

iPhylo: BLAST a sequence and get a tree | Virology and Bioinformatics from Virology.ca | Scoop.it

For this weeks sessions of my phyloinformatics course I'm developing some phylogeny tools. The first is a simple AJAX-based BLAST tool. I've always wanted a quick way to see a GenBank sequence in its phylogenetic context, so I've built a simple tool to that takes a GenBank accession number or GI number, submits a BLAST job, retrieves the sequences, aligns them using CLUSTALW, builds a quick and dirty neighbour-joining tree using PAUP*, then displays the tree using SVG (if your browser doesn't support this you won't see the tree). One use for this is to quikcly get a sense of whether an unnamed ("dark") taxon is related to sequences that have been identified.

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▶ Webinar: BLAST in the Cloud - YouTube

Presented July 30, 2014 and covering: an NCBI BLAST AMI at Amazon Web Services; introduction to AWS and setting up an instance; running command line BLAST an...
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SequenceServer: BLAST search made easy!

SequenceServer: BLAST search made easy! | Virology and Bioinformatics from Virology.ca | Scoop.it

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.

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