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- MiST String Genome sites IMG NMPDR Microbes Online P. denitrificans Proteins Pfam ExPASy PBIL TCoffee RNA Predict small RNA targets Secondary structure prediction...3 KB (7 words) - 19:48, 8 August 2007
- SCOP: Structural Classification of Proteins InterProScan: sequence search Pfam search PROSITE is a database of protein families and domains. It consists...4 KB (368 words) - 12:22, 19 June 2008
- motif box because it gives a much quicker answer and is a lot smaller than Pfam. More practice with these exercises will help in drawing more conclusions...6 KB (779 words) - 23:44, 2 November 2011
- are differences among GOS studies due to PFAM differences or because different organisms are there? The PFAM approach is a 'bag of genes' approach that...5 KB (697 words) - 22:24, 16 August 2017
- [48] Muscle [49] MAFFT [50] Kalign [51] PCMA [52] TBA MultiSeq [53] AL2CO PFAM InterPro CDD Thompson JD, Higgins DG, and Gibson TJ. CLUSTAL W: improving...1 KB (369 words) - 17:39, 18 March 2010
- structure databases, and family and domain databases gp120 itself is listed under Pfam, SUPFAM, and Gene3D features has been renamed 'sequence annotation' Includes...5 KB (983 words) - 06:12, 26 October 2011
- Protein Domain Envelope Glycoprotein gp160 (Q75760) protein; graphical view PFam gp120: PF00516 gp41: PF00517 gp160 env glycoprotein (graphical view): Q75760...12 KB (1,055 words) - 20:28, 22 October 2014
- Protein Domain Envelope Glycoprotein gp160 (Q75760) protein; graphical view PFam gp120: PF00516 gp41: PF00517 gp160 env glycoprotein (graphical view): Q75760...13 KB (1,365 words) - 17:30, 24 October 2014
- Compare to PFAM Compare to COGs or describe differences Finish statistical analyses Search vs. metagenomes and/or new genomes (compare to PFAM or COGs?)...2 KB (252 words) - 20:40, 7 August 2017
- combines prediction of Phobius, Pfam, LocaloDom (database of TM topologies and TM helix numbers of around 3,000 eukaryotic Pfam domains) The maximum number...56 KB (6,045 words) - 20:26, 21 November 2012
- current analysis pipeline How many Sfams have no Pfam annotation? Annotated Pfams: ~61% of Sfams have no Pfam Pfam-B families (unannotated): TBD What percent...3 KB (388 words) - 19:27, 7 August 2017
- databases (EvolutionaryTrace), and family and domain databases (Gene3D, InterPro, Pfam, SUBFAM, Protonet). See table under PTM / Processing. If you search on the...14 KB (1,307 words) - 21:45, 22 October 2014
- border="0"></a> <a href="http://pfam.sanger.ac.uk/"><img src="http://www.sanger.ac.uk/Software/Pfam/images/pfam_logo.gif" alt="pfam" border="0"></a> <a href="http://proteomics...7 KB (11 words) - 07:32, 7 November 2007
- databases? Which ones? Yes, there are links to PubMed and ProViz. Also, http://pfam.xfam.org, https://blast.ncbi.nlm.nih.gov/Blast.cgi Is it convenient to browse...9 KB (1,559 words) - 04:44, 2 April 2020
- Stephen's quality filtering Need to check for ncRNAs No PFAM-A annotation Other annotations: PFAM-B, other annotations in tables from UniProt Similar analysis...2 KB (342 words) - 19:44, 7 August 2017
- the reads. 3. Morgan: has been using Hummer version 3 (running GOS against pFAM) with genbeo, worked in 4 days. 4. Katie: talking about two things: 1) how...3 KB (490 words) - 21:55, 17 August 2017
- Tom: hot springs? EFI: novel gene families using Sfams Sfam sequences not in Pfam, KEGG, etc. Stephen & Patrick: Mapping Sfams to UniProt Intersecting with...1 KB (171 words) - 19:28, 7 August 2017
- will look at clusters that don't hit any previously described family (or in PFAM but no known function) Tom will subdivide existing families into subfamilies...4 KB (580 words) - 20:56, 16 August 2017
- clustering families based on shared Pfams Fuzzy clustering or network based on shared Pfams should be good enough Pfam to GO versus InterPro (better? slow...1 KB (197 words) - 20:42, 7 August 2017
- year Protein Db Families are mostly ready to go Need to do some testing vs. PFAM How well can one family be distinguished from another using profile HMMs...1 KB (232 words) - 22:27, 16 August 2017
