SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA […]
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BEReX is a new biomedical knowledge integration, search, and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PharmGKB, BioGRID, GO, HPRD, and MSigDB) and delineates an integrated network by combining the information available from these databases. Users search the integrated network by entering keywords and BEReX returns a sub-network matching the keywords. […] KEGG Pathway Pipeline: blastall -p blastp -d KEGG -i Haiyan.Pep.fasta -m 7 -a 10 -o Haiyan.Pep.fasta.blastp.m7 & ./tBLASTnParser.pl Haiyan.Pep.fasta.blastp.m7 Haiyan.Pep.fasta.blastp.m8 sed ‘1,1d’ Haiyan.Pep.fasta.blastp.m8 > Haiyan.Pep.fasta.blastp.m8.delhead /home/zhouzh/lib/454-2.5/bin/runAssembly -m -cpu 16 -cdna -nobig -o Test sff/GV1NGBM02.sff ./draw_png.py -i ACYPIprot.KO.file -p /home/shenzy/KEGG/ko_org -o map_result5 step 1: /home/soft/blast-2.2.23/bin/blastall -p blastp -d KEGG -i MBL_relation.fa -a 15 -b 30 […] When to use Mauve Contig Mover (MCM) The Mauve Contig Mover (MCM) can be used to order a draft genome relative to a related reference genome. The functionality of this software module has been described in Rissman et al. 2009 , a publication in Bioinformatics. The Mauve Contig Mover can ease a comparative study between […] the ‘new’ error message refers to a nonexistant Cairo library on your system, which is needed for the AnnotationSketch component of GenomeTools. If you do not need this, do a ‘make cleanup’ and recompile with the additional make option ‘cairo=no’, e.g. ‘make errorcheck=no cairo=no’. This will disable support for AnnotationSketch and remove the cairo […] Ok, I’ll do mine in English: go to UniProt.org. click tab “retrieve” Paste list into text box. Click Retrieve button. On results page, click FASTA download [ Download (30 KB*) | Open ] (Or you could click open just to have a look). http://circos.ca/documentation/ Tutorials and Course The tutorials serve as a walkthrough through Circos. The course is a more structured set of materials that takes you through creating an image from scratch. The tutorials act as documentation — each lesson presents a specific feature of Circos. Example Image Once you download and install Circos, # install circos […] Our project TaxCollector has been published in MPDI Diversity. Abstract The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II) and the Greengenes Project offer access […] http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html mcaGUI Microbial Community Analysis GUI Bioconductor version: Release (2.10) Microbial community analysis GUI for R using gWidgets. Author: Wade K. Copeland, Vandhana Krishnan, Daniel Beck, Matt Settles, James Foster, Kyu-Chul Cho, Mitch Day, Roxana Hickey, Ursel M.E. Schutte, Xia Zhou, Chris Williams, Larry J. Forney, Zaid Abdo, Poor Man’s GUI (PMG) base code by […] http://bib.oxfordjournals.org/content/13/4/495.full Key Points Vast amounts of variation data from genome sequencing studies need to be analyzed to understand its association with various phenotypes. Well-curated databases, reliable tools for gene prioritization and accurate methods for predicting the impact of variants will be essential for the interpretation of personal genomes. Standard and unified protocols […] |
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