Blast

Jalview - Java alignment editor. Omega - fast, accurate, scalable multiple sequence alignment for proteins. "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. A full description of the algorithms used by Clustal Omega is available in the Molecular Systems Biology paper Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Clustal Omega can be run online at the following websites (this list will expand in the coming months). Please that webservers may have limitations on maximum alignment size not present in the standalone version.

Help Citing Clustal View ChangeLog News: Clustal Omega Results. Python.bio.general - [BioPython] Blast to genome specific databases? - msg#00037. Thread at a glance: Previous Message by Date: Re: [BioPython] deleting and inserting 'chains' in Bio.PDB Thanks!

And thank you, Thomas, for your wonderful module! The module is actually easy to use, despite of my questions ... ;-) Cheers, Christian On Mon, 2007-08-20 at 17:51 +0200, Thomas Hamelryck wrote: > On 8/20/07, Christian Meesters <meesters@xxxxxxxxxxxx> wrote: > > Hi, > > > > I'd like delete and insert subunits in my structure object. Next Message by Date: Re: [BioPython] Blast to genome specific databases? If you follow the directions on this page: you should be able to modify the URLAPI DATABASE parameter to that in the list; another option would be to limit the results to a specific taxid (like 9606) using the ENTREZ_QUERY.

Previous Message by Thread: Re: [BioPython] qblast Next Message by Thread: BLAST Program Selection Guide. Pattern-Hit Initiated (PHI)-BLAST is designed to search for proteins that contain a pattern specified by the user AND are similar to the query sequence in the vicinity of the pattern.

This dual requirement is intended to reduce the number of database hits that contain the pattern, but are likely to have no true homology to the query. To run PHI-BLAST, enter your query (which contains one or more instances of the pattern) into the "Search" box, and enter your pattern into the "PHI pattern" box in the "Options" section of the page. Patterns must follow the syntax conventions of PROSITE. Only one pattern can be used in a given search. Pattern syntax is described here. An example query sequence and a sample pattern in ProSite format are given below for test run with PHI-BLAST.

[LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV]. 's URL API. User's Guide. 8.6 Sample Script in Perl. BLAST Frequently Asked questions. BLAST Frequently Asked questions. Urlapi.pdf.