Tools to detect synteny blocks regions among multiple genomes
...is an automated system for identifying and displaying genome synteny alignments. The genomes may be represent...Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between speci...2602 days ago
Software and Tools to detect structure variation with long reads !!
...tural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and c...2599 days ago
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Alignment of closely related whole genomes/scaffolds
...ngth, to aid in the study of populations, pan-genomes, and genome evolution.This bookmaks have been created to report new tools for whole genome alignments. Please report new whole gen...3011 days ago
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Bio++ : C Language libraries for your biological need
...NA, RNA, Proteins, Codons, any 'Word' of a given size).Several containers available for inner storage, with several implementations. Support for alignments.Various I/O formats supported...3939 days ago
Genome Assembly Tools and Software - PART2 !!
...am data analysis by relieving investigators from the burdens of data preparation. SAMMate 2.7.4 / assemblySAM 1.1 – Processing Short Read Alignments in SAM/BAM format / RNA-Seq A...2677 days ago
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List of bioinformatics open source projects/software.
...e given assigned Residual Dipolar Coupling data SAM Tools Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments Staden Package Sequence ass...3748 days ago
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Des Higgins: Visualizing Multiple Sequence Alignments
...y-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of s...llenge, including faster algorithms and abstract views of clusters of alignments. This talk was presented at V...3713 days ago
Comparative Genomics in Ensembl
The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences. Learn how to view and export these data in this video.3384 days ago
BASH script for SelfBLAST a genome
...n echo "You want entire sequence to blast" SEQ=$FASTAFILE else echo "Something went wrong $USER - Contact jitendra" fi echo "Doing alignments -- BLASting"; blastn -task m...2644 days ago
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Understanding reads mapping and flags !
Linear Alignment: An alignment of a read to a single reference sequence that may include insertions, deletions, skips and clipping, but may not include direction changes (i.e. one portion of the alignment on forward strand and another portion of alignment on reverse strand). ...Tags: Linear, Chimeric, Supplementary, Primary, Secondary, Alignments
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Comment on "Basic command-line to run BLAST"
..."words," and searching for matches to those words in the database. It then expands the matches to identify longer regions of similarity, called "alignments," and calculates a score for...412 days ago
Comment on "Tools to detect synteny blocks regions among multiple genomes"
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments https://pubmed.ncbi.nlm.nih.gov/32463100/1236 days ago