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...sive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted i...2874 days ago
Bioinformatics tools and software
...gnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW. UPARSE >OTU clustering for 16S and other marker genes. Hig...2873 days ago
- Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM for...
2865 days ago
- ...n a single sequenced genome or a small set of genomes, you need to call your data against a background population, such as a set of genomes from the 1000 Genomes Project. The...
2810 days ago
- ...m for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MG...
2811 days ago
- ...f biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads. KisSplice is not a...
2831 days ago
- ...sessment of de novo genome assemblies Citation This software is fully described in the paper:Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality as...
2823 days ago
- ...iscovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6): R84. doi:10.1186/g...
2822 days ago
GeneValidator - Identify problems with predicted genes
...Dragan M‡, Moghul MI‡, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015....2821 days ago
- ...astacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation...tp://longlab.uchicago.edu/?q=gKaKs http://www.ncbi.nlm.nih.gov/pubmed/23314322
2817 days ago
