The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

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 taxon[……]

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BEReX : Biomedical Entity-Relation eXplorer

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 th[……]

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KEGG annotation pipeline

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/ru[……]

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Reordering contigs in draft genomes by MAUVE

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 com[……]

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Install genometools

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 di[……]

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Batch download sequences from uniprot based on protein names

Ok, I’ll do mine in English:

  1. go to UniProt.org.
  2. click tab “retrieve”
  3. Paste list into text box. Click Retrieve button.
  4. On results page, click FASTA download [ Download (30 KB*) | Open ] (Or you could click open just to have a look).

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Circos 安装和学习 (一)

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 Circo[……]

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TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels

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 Da[……]

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Microbial Community Analysis GUI–Bioconducter

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-Ch[……]

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Bioinformatics for personal genome interpretation

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[……]

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