Most Commonly used Awk by Bioinformatician
Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with P...3904 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...paration facilitates improved mapping and assembly of GC-biased genomes. Kozarewa et al, Nature Meth...pression estimation with read mapping uncertainty. Li et al, Bioin...r rapid and efficient genetic mapping. Andolfatto et al. Genome Res...ty of California - Santa Cruz Genome Browser is on the FAQ list A...3771 days ago
List of bioinformatics open source projects/software.
Open source software is software that can be freely used, changed, and shared (in modified or unmodified form...information about biological sequences collected from the environment. GenomeSpace http://www.genomes...3749 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
List of generic simulation software/tools/resource with brief desc...LF A Simulation Framework for Genome Evolution http://www.cbrg.eth...on test bed for hypotheses of genome evolution http://acb.qfab.org...ts/gametes/?source=navbarGASP Genometric Analysis Simulation Progr...3729 days ago
List of In-silico Binding Site Prediction Tools
Following are the list of In-silico Binding Site Prediction in Proteins tools CASTp : http:...ar Interactions Server. For a given protein sequence or structure query, IBIS reports physica...3736 days ago
Perl one-liner for bioinformatician !!!
With the emergence of NGS technologies, and sequencing data most of the bioinformaticians mung and wrangle around m...://genomics-array.blogspot.in/2010/11/some-unixperl-oneliners-for.html http://genomes...3620 days ago
Next generation sequencing in R or bioconductor environment
There are many R software and bioconductor packages for NGS data analysis,...s, rtracklayer, GenomicFeatures and BSgenome. Compared to the IRange...for SNP analysis: snpMatrix BSgenome BSgenome provides an object...s the biomaRt, IRanges, Biostrings, BSgenome,...3617 days ago
Commercial and public next-gen-seq (NGS) software
...na reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu.../mummer.sourceforge.net/) The mapping short reads called gnumap (ht...zner from UCSD. (published in Genome Research)RMAP (A program for m...er" Transcriptomics ERANGE - Mapping and Quantifying Mammalian Tra...3511 days ago
Using Interval Trees to Query Genome Annotations by Position
To work on query related to overlapping genomic features: use IntervalTree python pkg http://informatics.malariagen.net/2011/07/07/using-interval-trees-to-query-genome-...3541 days ago
Apps for Busy Bioinformatics Researchers !!!
DNAApp: DNAApp: for iPhone/iPad This is an iOS app that allows for...t that offers protein-protein physical/enzymatic interaction infor...KEGG, PubMed, SymAtlas, UCSC genome browser, Pathway Commons, Gen...p/geneindex/id319769866?mt=8 Genome Voyager: iPad Gain first han...3533 days ago