Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does th....g. this by David Eccles ./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq...2128 days ago
List of motif discovery tools !
...-footprint -- database of DNA-binding protein structures Find binding specificity information about...es. CSA -- The Catalytic Site Atlas To search for catalytic r...uence. E1DS -- catalytic site prediction based on 1D signature...h approach to protein-binding sites analysis Predict the locati...2005 days ago
Useful links to therapy, disease, drug and drug-target network data:
...ase of human genes and genetic disorders http://www.ncbi.nlm.nih.gov/ sites/entrez?db=omim PDTD: 3D drug...al/ [25] Protein ligand network: a network of 4208 ligands and ~15000 binding sites http://pbil.kaist.ac.kr/~par...1446 days ago
Protocol for De novo Genome Assembly using Illumina Reads
In this protocol, we address and describe the de novo assembly method for small to...m/p/ngopt/wiki/How_To_Score_Genome_Assemblies_with_MauveInGAP-SV - https://sites.google.com/site/nextgengenomics/ingap and htt...1216 days ago
Ancient whole genome duplication (WGD) detection tools !
There are two methods for ancient WGD detection, one is col...mber of synonymous substitutions at each synonymous site, and there is also a Ka corre...non-synonymous substitutions at each non-synonymous site. At present, some people hav...1167 days ago
List of comparative genomics resources !
...c -- a whole genome resource for the detection of transcription factor binding site clusters associated with conv...SwissRegulon -- a database of genome-wide annotations of regulatory sites Search for genome-wide anno...689 days ago