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• Reference Indexes
  ...rence indexes built for the respective tools using the appropriate genomic sequence data. This page provides a short overview of our reference index building p ...most reference indexes to be built. In that case we'll use the non-masked sequence.
  2 KB (361 words) - 20:30, 12 August 2022
• Consed
  calling, sequence comparisons, and sequence assembly. Phred, Cross_match, Consed/Autofinish is a tool for viewing, editing, and finishing sequence assemblies created with phrap. Finishing capabilities include allowing the
  3 KB (348 words) - 18:39, 12 August 2022
• UCSC
  ...ion tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loa
  3 KB (349 words) - 20:53, 12 August 2022
• WGS Assembler
  ...n sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celer
  3 KB (359 words) - 20:56, 12 August 2022
• SRAssembler
  ...cal assembly of genomic regions matching a homologous query protein or DNA sequence. ...ssembler first collects the reads that can be locally aligned to the query sequence and assembles them into contigs. Additional reads are then found by alignin
  3 KB (381 words) - 15:33, 27 May 2022
• Kalign
  Kalign is a fast multiple sequence alignment program for biological sequences. "Kalign 3: multiple sequence alignment of large data sets."
  2 KB (265 words) - 19:28, 12 August 2022
• USEARCH
  ...tions, including E-values, identity, coverage (fraction of query or target sequence covered by the alignment) and maximum gap length, and a range of output fil ...RCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude
  4 KB (559 words) - 17:19, 22 August 2022
• PRINSEQ
  ...n in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
  2 KB (271 words) - 15:52, 10 June 2022
• Wgs
  ...n sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celer
  3 KB (375 words) - 20:55, 12 August 2022
• Nt
  This repo contains a set of neural transducer, e.g. sequence-to-sequence model, focusing on character-level tasks. It powers several papers and work
  2 KB (262 words) - 14:38, 15 July 2022
• MHAP
  ...rithm. Designed to efficiently detect all overlaps between noisy long-read sequence data. It efficiently estimates Jaccard similarity by compressing sequences
  2 KB (270 words) - 16:15, 10 June 2022
• SEQPower
  SEQPower provides statistical power analysis and sample size estimation for sequence-based association studies. ...tez, B. Peng and S. M. Leal, Power analysis and sample size estimation for sequence-based association studies. Bioinformatics. (2014)]
  2 KB (274 words) - 22:38, 21 August 2022
• GHOST-MP
  ...ches for similar sequences among nucleotide query sequences and amino acid sequence database like BLASTX. GHOST-MP runs on a distributed memory system and proc
  2 KB (285 words) - 20:11, 7 May 2020
• Shasta
  ...of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer re
  3 KB (402 words) - 21:24, 6 December 2019
• Ont tutorial cas9
  ...t enrichment strategy. This workflow is suitable for Oxford Nanopore fastq sequence collections and requires a reference genome and a BED file of target coordi
  2 KB (289 words) - 18:38, 2 June 2022
• Tcoffee
  T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine th T-Coffee: A novel method for multiple sequence alignments.
  2 KB (280 words) - 20:46, 12 August 2022
• NCBI GenBank Tools
  ..., 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), t
  2 KB (291 words) - 14:33, 19 August 2022
• ProDy
  ...s for comparative analysis and modeling of protein structural dynamics and sequence co-evolution. Fast and flexible ProDy API is for interactive usage as well
  2 KB (294 words) - 19:38, 21 August 2022
• Newbler
  ...de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454
  2 KB (305 words) - 16:17, 19 August 2022
• Rvtests
  ...tests, is a flexible software package for genetic association analysis for sequence datasets. ...ficient and Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426.]
  3 KB (293 words) - 21:59, 21 August 2022
• GeneMarkS
  ....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.
  2 KB (296 words) - 16:45, 27 May 2022
• BloomTree
  The Sequence Bloom Tree (SBT) is a method that will allow you to index a set of sequence. The code base provided here is an implementation of SBT written in
  3 KB (302 words) - 16:49, 10 June 2022
• MetaGeneMark
  ....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.
  2 KB (298 words) - 21:22, 6 December 2019
• GeneMarkS-T
  ....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions.
  2 KB (296 words) - 17:25, 2 June 2022
• DEXTRACTOR
  RS II sequencer. Generally speaking, this information is the sequence of all the reads to produce a highly accurate consensus sequence as the last step in the assembly
  3 KB (441 words) - 19:20, 10 June 2022
• HAPCUT
  ...ts, and outputs the phased haplotype blocks that can be assembled from the sequence reads.
  2 KB (298 words) - 18:13, 15 August 2022
• Ncbi cli
  Use it to find and download sequence, annotation, and metadata for genes and genomes Use '''datasets''' to download biological sequence data across all domains of life from NCBI.
  3 KB (306 words) - 15:47, 9 June 2023
• Fairseq
  Fairseq(-py) is a sequence modeling toolkit that allows researchers and developers to train custom mod A Fast, Extensible Toolkit for Sequence Modeling. Myle Ott and Sergey Edunov and Alexei Baevski and Angela Fan and
  3 KB (296 words) - 15:18, 15 August 2022
• YASRA
  ...improve the performance, both in runtime and quality for 454 and Illumina sequence reads.
  3 KB (304 words) - 20:56, 12 August 2022
• GeneMark-ES
  ....hmm (P and E) programs identify the maximum likely parse of the whole DNA sequence into protein coding genes (with possible introns) and intergenic regions. F
  3 KB (303 words) - 16:44, 27 May 2022
• MMseqs2
  ...ing) 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 L ...Soeding J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics, doi: 10.1093/bioinformatics/bty1057 (2019).]
  3 KB (413 words) - 20:22, 2 October 2023
• Wise
  ...e focused on comparisons of biopolymers, commonly DNA sequence and protein sequence. There are many other packages which do this, probably the best known being
  3 KB (321 words) - 21:29, 6 December 2019
• SNP-Pipeline
  SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced fr ...ne: an automated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20 https://doi.org/10.7717/peerj-cs.20]
  3 KB (306 words) - 17:00, 10 June 2022
• Catch
  ...ackage for designing probe sets to use for nucleic acid capture of diverse sequence. of species. It allows blacklisting sequence from the design (e.g., background in microbial enrichment),
  3 KB (422 words) - 18:23, 12 August 2022
• DeconSeq
  The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configur ...med/21278185 Schmieder R and Edwards R: Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 2011, 6:e1728
  3 KB (299 words) - 17:00, 10 June 2022
• Recycler
  ...from sequence data of isolate microbial genomes, plasmidome and metagenome sequence data.
  3 KB (297 words) - 14:21, 11 October 2022
• FSA
  ...using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise com
  3 KB (307 words) - 20:38, 23 May 2022
• Ancestryhmm
  ...neously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. ...neously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy. PLoS genetics, 13(1), p.e1006529.
  2 KB (291 words) - 21:25, 9 May 2023
• AliStat
  Multiple sequence alignments may contain a variety of completely-specified characters. Here a for multiple sequence alignments. NAR Genomics and Bioinformatics 2 (2), lqaa024.
  3 KB (315 words) - 20:18, 1 October 2020
• REPdenovo
  REPdenovo is designed for constructing repeats directly from sequence reads. It based on the idea of frequent k-mer assembly. REPdenovo provides ...elsen and Yufeng Wu, REPdenovo: Inferring de novo repeat motifs from short sequence reads, PLoS One 11.3 (2016): e0150719.]
  3 KB (327 words) - 21:43, 21 August 2022
• SeSiMCMC
  The Sequence Similarities by Markov Chain Monte Carlo (SeSiMCMC) algorithm careful Bayesian analysis to consider site absence in a sequence.
  3 KB (299 words) - 22:41, 21 August 2022
• HLAminer
  ...and align the resulting contigs to reference HLA alleles from the IMGT/HLA sequence repository using commodity hardware with standard specifications (<2GB RAM, ...novo assembly of all recruited reads, a set of contigs is generated. Only sequence contigs equal or larger than 200nt in length are considered for further ana
  4 KB (541 words) - 14:55, 14 December 2022
• Magus
  MAGUS is a tool for piecewise large-scale multiple sequence alignment. Original MAGUS paper: Smirnov, V. and Warnow, T., 2020. MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics. https://doi.org/10.1093/b
  3 KB (327 words) - 17:51, 16 March 2022
• CRISP
  ...d using the Illumina sequencing platform. In principle, it should work for sequence data from other sequencing platforms. The method requires each pool to be s
  3 KB (342 words) - 21:01, 6 December 2019
• MetaCluster
  ...nomic sequences. Existing binning methods based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorg
  3 KB (321 words) - 19:26, 18 August 2022
• RSeQC
  ...put sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-se
  3 KB (328 words) - 17:48, 10 June 2022
• Barrnap
  ...more CPUs. Running time is approximately 1 second per 1 megabase of input sequence.
  3 KB (328 words) - 17:55, 10 June 2022
• ProtExcluder
  ...ude the portion of DNA sequence (as well as certain length of the flanking sequence – given by the user, default = 50 bp) matching subjects in a protein data
  3 KB (329 words) - 21:22, 6 December 2019
• Bridger
  ...r to search an optimal set of paths (transcripts) that can be supported by sequence data and could explain all observed splicing events of each locus.
  3 KB (341 words) - 13:14, 15 August 2022
• Last
  * Handle big sequence data, e.g: * Use sequence quality data properly.
  3 KB (342 words) - 19:29, 12 August 2022

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