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MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Manisha Mishra 1407 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...NextDenovo: string graph-based de novo assembler for TGS long reads
By Jit 1786 days agogithub.com - NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 2544 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...CLARK: Fast, accurate and versatile sequence classification system
By Jit 1745 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Abhi 1146 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 261 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,...Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
By Jit 2559 days agosourceforge.net - Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the...Many-to-many pairwise alignments of two sequence sets
By Poonam Mahapatra 2351 days agoemboss.sourceforge.net - needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...iRNAD: a computational tool for identifying D modification sites in RNA sequence
By Abhimanyu Singh 2020 days agolin-group.cn - iRNAD, for identifying D modification sites in RNA sequence. In this predictor, the RNA samples derived from five species were encoded by nucleotide chemical property and nucleotide density. Support vector machine was utilized to perform the...Apollo: a sequence annotation editor
By Abhimanyu Singh 1917 days agogenomebiology.biomedcentral.com - The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting...
