phantome.org
PhAnToMeRs
http://www.phantome.org/index.php/phantomers
Phage Annotation Tools and Methods. All phages in the PhageSeed. Lytic and Lysogenic Phage. This section lists all who are working with the PhAnToMe project: developers, annotators, data generators, and consultants. Official PhAnToMers (Founding clone). Created: 01 September 2009. Last Updated: 19 November 2012. Written by Ramy K. Aziz. Robert A. Edwards. Seed development and maintenance. BioBike development and maintenance. Phage sequencing and comparative genomics. Ramy K. Aziz. Created: 01 March 2010.
hmpdacc.org
Human Microbiome Project DACC - Tools & Protocols
http://www.hmpdacc.org/resources/tools_protocols.php
Login not recognized, please retry. Login not recognized, please retry. How did you hear about the HMP/DACC? Poster and Booth at ASM 2016. Metagenome Analysis Workshop March 3-6. IHMC 2015 from Mar. 31 to Apr. 2. Cutaneous microbiome effects of fluticasone propionate cream and adjun. GABA-producing Bifidobacterium dentium modulates visceral sensitivity . Mobile genes in the human microbiome are structured from global to ind. NCBI HMP Data Repository. Funded Tools and Technology Research. A fully-automate...
theseed.org
SpecialPurposeDBs - TheSeed
http://www.theseed.org/wiki/SpecialPurposeDBs
Home of the SEED. EGGS database: Essential Genes on Genome Scale. Retrieved from " http:/ / /w/index.php? Home of the SEED. Scan for Matches (patscan). FAQ Frequently Asked Questions. This page was last modified on 6 January 2009, at 10:39. This page has been accessed 10,509 times.
theseed.org
Annotating 1000 genomes - TheSeed
http://www.theseed.org/wiki/Annotating_1000_genomes
Home of the SEED. A manifesto written in early 2004. The Project to Annotate the First 1000 Sequenced Genomes, Develop Detailed Metabolic Reconstructions, and Construct the Corresponding Stoichiometric Matrices. The Project to Annotate 1000 Genomes. We now proceed to describe the details of the three stages. Stage 1: Development of Initial Encodings of Subsystems. Stage 2: The Use of True Experts and the Wet Lab to Refine the Encodings. Filling in the Missing Pieces. The Project to Annotate 1000 Genomes.
bytesizebio.net
Resources | Byte Size Biology
http://bytesizebio.net/resources
The musings and ravings of a computational biologist about science, computers, music and, you know, stuff. I need one page to collate software and docs I come across, and that is or might be useful to me. Let’s hope this does not become a total mess, and would be useful to others. Nick Loman’s xbase. For short read annotation and assembly. This goes hand in hand with his sage advice page. Also, this document from Illumina. Standardized velvet assembly report. For genomes and metagenomes respectively.
pathogenportal.org
Pathogen Portal
http://www.pathogenportal.org/portal/portal/PathPort/About
Pathogen Portal is a repository linking to the Bioinformatics Resource Centers (BRCs) sponsored by the National Institute of Allergy and Infectious Diseases (NIAID) and maintained by The Virginia Bioinformatics Institute. The BRCs are providing web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. About the Bioinformatics Resource Centers. Stores, updates, integr...
thegenomefactory.blogspot.com
The Genome Factory: March 2013
http://thegenomefactory.blogspot.com/2013_03_01_archive.html
Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia. Saturday, 30 March 2013. Bacterial genome annotation systems. You get a bacterial isolate. You sequence it. You manage to get some contigs after mucking around with some de novo. Assembly software. Now what? What is genome annotation? A gene abbreviation and an enzyme classification number. In the old days, a basic ORF. Finder would be run over the contigs. Then the ...
thegenomefactory.blogspot.com
The Genome Factory: Bacterial genome annotation systems
http://thegenomefactory.blogspot.com/2013/03/bacterial-genome-annotation-systems.html
Bioinformatics tips, tricks, tools and commentary with a microbial genomics bent. Written by Torsten Seemann from Melbourne, Australia. Saturday, 30 March 2013. Bacterial genome annotation systems. You get a bacterial isolate. You sequence it. You manage to get some contigs after mucking around with some de novo. Assembly software. Now what? What is genome annotation? A gene abbreviation and an enzyme classification number. In the old days, a basic ORF. Finder would be run over the contigs. Then the ...
connorskennerton.wordpress.com
Blog | Connor Skennerton | Biologist, Bioinformatician
https://connorskennerton.wordpress.com/blog
November 19, 2016. Downloading NCBI genomes from a given taxonomy. Toolkit is great for programmatic access to all of NCBI’s resources. This little snippet below finds all of the refseq representative genomes for a given NCBI taxonomy ID, makes a little summary of the genomes downloaded and uses. To download the genbank files from the Assembly FTP. Change the inital query in the first call to. To change what genomes are downloaded. November 16, 2016. November 16, 2016. SMSP, DSM 22288. There are exce...
