Jit
Enthusiast computational biologist with business dream !!!
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Awesome perl frameworks, libraries and software - PART 3
Last updated 2700 days ago by Neelfujiwara/perl-queue-q4pg-lite - simple message queue using PostgreSQL. formbuilder/formbuilder - Perl CGI::FormBuilder module for generating, validating, and processing HTML forms fastly/fastly-perl - Fastly perl...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2380 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...AnchorWave
By Neel 1008 days agogithub.com - AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor...MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly
By Abhi 172 days agometagraph.ethz.ch - The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle,...Quota synteny alignment
By Jit 2676 days agogithub.com - Typically in comparative genomics, we can identify anchors, chain them into syntenic blocks and interpret these blocks as derived from a common descent. However, when comparing two genomes undergone ancient genome duplications (plant genomes in...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2395 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
By Poonam Mahapatra 2370 days agomolevol.cmima.csic.es - Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
By Jit 2287 days agowww.ncbi.nlm.nih.gov - Mulan: Multiple-sequence local alignment and visualization for studying function and evolution Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional...MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 1967 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 263 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...
