Search results

• Category:Alignment
  Biological sequence alignment tools and documentation
  24 members (0 subcategories, 0 files) - 15:24, 23 August 2022
• WebLogo
  WebLogo is an application designed to make the generation of sequence logos as easy and painless as possible. ...precise description of, for example,a binding site, than would a consensus sequence.
  3 KB (417 words) - 17:40, 22 August 2022
• Category:Assembly
  Short Sequence Assembly software.
  20 members (0 subcategories, 0 files) - 15:24, 23 August 2022
• Infernal
  Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a
  3 KB (305 words) - 19:31, 24 August 2022
• EvoLSTM
  ...robabilities. EvoLSTM brings modern machine-learning approaches to bear on sequence evolution. It will serve as a useful tool to study and simulate complex mut
  3 KB (309 words) - 18:52, 12 August 2022
• Sim4
  ...verlaps the end of the other). If seqfile2 is a database of sequences, the sequence in seqfile1 will be aligned with each of the sequences in seqfile2.
  2 KB (302 words) - 20:41, 12 August 2022
• RNAsalsa
  ...e, that RNAsalsa uses structure information for adjusting and refining the sequence alignment and vice versa.
  3 KB (368 words) - 21:24, 6 December 2019
• Spruceup
  ...ts (alignment rows), which is different from the problem of poorly aligned sequence blocks (alignment columns) commonly addressed by alignment trimming softwar ...identification, visualization, and removal of outliers from large multiple sequence alignments. Journal of Open Source Software, 4(42), 1635, https://doi.org/1
  3 KB (317 words) - 21:24, 6 December 2019
• CD-HIT
  ...-hit produces a set of closely related protein families from a given fasta sequence database.
  3 KB (354 words) - 18:24, 12 August 2022
• SuperCRUNCH
  ...orking with phylogenetic datasets. SuperCRUNCH can be run using any set of sequence data, as long as sequences are in fasta format with standard naming convent ...s (adjust sequence directions, adjust reading frames), several options for sequence alignment (Clustal-O, MAFFT, Muscle, MACSE), and multiple options for align
  4 KB (499 words) - 14:47, 11 May 2020
• RepeatMasker
  sequence as well as a modified version of the query sequence in which On average, almost 50% of a human genomic DNA sequence currently will
  2 KB (325 words) - 20:32, 12 August 2022
• Minigraph
  ...graph constructor. It finds approximate locations of a query sequence in a sequence graph and incrementally augments an existing graph with long query subseque
  2 KB (279 words) - 18:08, 31 March 2021
• Sputnik
  ...the resulting hits are written to stdout along with their position in the sequence, length, and a score determined by the length of the repeat and the number
  2 KB (311 words) - 15:50, 22 August 2022
• FAST
  ...BioPerl FastA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm.
  3 KB (358 words) - 21:21, 6 December 2019
• Artemis
  ...next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. ...: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
  3 KB (378 words) - 14:53, 12 August 2022
• Mlstcheck
  ...for each locus, and the ST (or nearest ST), the other contains the genomic sequence for each allele. ...us, the contaminated flag is set. Optionally you can output a concatenated sequence in FASTA format, which you can then use with tree building programs. New, u
  3 KB (395 words) - 18:06, 27 May 2022
• TNTBLAST
  ...ideally) match experimental PCR results. To enable searching of very large sequence databases (i.e. all of Genbank), ThermonucleotideBLAST can use run-time dat
  3 KB (385 words) - 20:08, 2 June 2022
• Seq crumbs
  seq_crumbs aims to be a collection of small sequence processing utilities. ...and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utili
  3 KB (328 words) - 15:12, 27 May 2022
• HMMER
  HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods
  3 KB (397 words) - 18:18, 15 August 2022
• Impg
  impg (Implicit Pangenome Graph) projects sequence ranges through many-way (e.g. all-vs-all) pairwise alignments built by tool ...htforward to use to extract FASTA sequences for downstream use in multiple sequence alignment (like mafft) or pangenome graph building (e.g., pggb or minigraph
  3 KB (392 words) - 21:22, 10 April 2024
• 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

View (previous 50 | next 50) (20 | 50 | 100 | 250 | 500)