mobyle.pasteur.fr

smallchangebio.wordpress.com

Small Change Bioinformatics | Page 2

https://smallchangebio.wordpress.com/page/2

July 11, 2014. Notes: Bioinformatics Open Source Conference 2014 day 2: Philip Bourne, Software Interoperability, Open Science. I’m at the 2014 Bioinformatics Open Source Conference (BOSC). In Boston. It’s a great two day conference devoted to open source, science and community. These are my notes from the day 2 morning session. Next Day Video. Recorded all the talks and they’re available on the Open Bio video site. Biomedical Research as an Open Digital Enterprise. Mentions the current issue that softwa...

clustal.org

Clustal Omega - fast, accurate, scalable multiple sequence alignment for proteins

http://www.clustal.org/omega

The last alignment program you'll ever need". Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. Please note that Clustal Omega is currently a command line-only tool.

emboss.open-bio.org

EMBOSS Users Guide

http://emboss.open-bio.org/html/use/index.html

EMBL European Bioinformatics Institute. EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. EMBL European Bioinformatics Institute. EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. EMBL European Bioinformatics Institute. EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. 1 Introduction to EMBOSS. 3 About the Authors. 4 How To Cite EMBOSS. Conventions used in the Manual. 1 Command Line Sessions and Commands. 2 Program Listings and Code.

bcbio.wordpress.com

Summary from Bioinformatics Open Science Codefest 2013: Tools, infrastructure, standards and visualization | Blue Collar Bioinformatics

https://bcbio.wordpress.com/2013/07/18/summary-from-bioinformatics-open-science-codefest-2013-tools-infrastructure-standards-and-visualization

Summary from Bioinformatics Open Science Codefest 2013: Tools, infrastructure, standards and visualization. The 2013 Bioinformatics Open Source Conference (BOSC). Starts tomorrow in Berlin, Germany. It’s a yearly conference devoted to community-based software development projects supporting biological research. Members of the Open Bioinformatics Foundation. Discuss implementations and approaches to better provide interoperable and reusable software, libraries and pipelines. Kindly hosted Codefest 2013.

tcoffee.crg.cat

T-COFFEE Multiple Sequence Alignment Server

http://tcoffee.crg.cat/apps/tcoffee/index.html

Combine popular aligners (M-Coffee). Combine popular aligners (M-Coffee). Combine popular aligners (M-Coffee). Homologous promoter regions (Pro-coffee). Evaluates your Alignment and outputs a Colored version indicating the local reliability. Cite. Evaluates Multiple Sequence Alignment using structural information with APDB and iRMSD. Cite. Allows fine-grained structural clustering of a given group of related protein domains. Evaluation of protein MSAs using a single 3D structure Cite. IGS lab., CNRS.

tcoffee.crg.cat

T-COFFEE Multiple Sequence Alignment Server

http://tcoffee.crg.cat/apps/tcoffee

Combine popular aligners (M-Coffee). Combine popular aligners (M-Coffee). Combine popular aligners (M-Coffee). Homologous promoter regions (Pro-coffee). Evaluates your Alignment and outputs a Colored version indicating the local reliability. Cite. Evaluates Multiple Sequence Alignment using structural information with APDB and iRMSD. Cite. Allows fine-grained structural clustering of a given group of related protein domains. Evaluation of protein MSAs using a single 3D structure Cite. IGS lab., CNRS.

lifesciinformatics.blogspot.com

Asif M. Khan: A Practical Bioinformatician's Advance Toolkit

http://lifesciinformatics.blogspot.com/2007/12/practical-bioinformaticians-advance.html

Asif M. Khan. Life Science Informatics Resource Hub. A Practical Bioinformatician's Advance Toolkit. An integrated portal for diverse type of sophisticated bioinformatics analyses (highly recommended). Construct and analyze structural variants. Multiple sequence alignment program for the whole-genome human-mouse alignments. Prediction of Functional Effect of Human nsSNPs. Sorting Intolerant from Tolerant. Assigns Molecular Functional Effects of Non-Synonymous SNPs Based on Structure and Sequence Analysis.

support.geneious.com

Analyze / optimize sequences for expression systems : Geneious Support

https://support.geneious.com/entries/22232396-Analyze-optimize-sequences-for-expression-systems

Check your existing requests. Analyze / optimize sequences for expression systems. Suggested this on October 23, 2012, 05:38. This feature was added in R7. You can access it via Optimize Codons. In the Annotate and Predict menu. Please post any feedback or suggestions for improvement here. October 23, 2012, 07:51. I'm trying to find a work arround for finding rare codons. Can genious even select a type of codon. Lets say I want to find all AGA, but only in one frame. November 10, 2012, 07:21. It basicall...

onubiol217.blogspot.com

ONU Biology 217: Module 4, Lab 14 - BioinformaticsA simple bioinformatics pipeline to infer a phylogeny

http://onubiol217.blogspot.com/2011/02/module-4-lab-13-bioinformatics-simple.html

What happens in the 'Introduction to Molecular Biology' (BIOL 217) class at Ohio Northern University in Ada, OH. Thursday, February 10, 2011. Module 4, Lab 14 - Bioinformatics. A simple bioinformatics pipeline to infer a phylogeny. A 'good' electropherogram of the RRss gene from an earthworm (. And a 'bad' electropherogram of RRss gene of a cnidarian (. Click pic for a full size view). During this lab students followed a simple bioinformatics pipeline. Using an on-line version of ClustalW. Web portal&#46...

mafft.cbrc.jp

MAFFT - a multiple sequence alignment program

http://mafft.cbrc.jp/alignment/software

Multiple alignment program for amino acid or nucleotide sequences. MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of ∼200 sequences), FFT-NS-2 (fast; for alignment of ∼30,000 sequences), etc. The latest version is 7.304 (2016/Aug/12). Fasta format. example1 (LSU rRNA). The type of input sequences (amino acid or nucleotide) is automatically recognized. If not sure which option to use,. A simp...