AVID: A Global Alignment Program
...We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We ha...2582 days ago
Synteny Portal: a web-based application portal for synteny block analysis
...synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visual...2582 days ago
dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation
...y of automated and comprehensive CAZyme annotation of a given genome submitted by the user; dbCAN...n in all the relevant full-length CAZyme proteins in all sequenced genomes; dbCAN provides the most co...2577 days ago
Genome Annotation Transfer Utility (GATU)
Genome Annotation Transfer Utility (GATU)...ck, efficient annotation of similar genomes using genomes that have already been annot...hms to map genes from the reference genome (the annotated strain) to the...it was designed for use with viral genomes, GATU can also be used to he...2577 days ago
NovelSeq: Novel Sequence Insertion Detection
The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/203857262566 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
...even with default parameters. Circular genome handling to resolve coverage drops near ends of the genome. E-value.&n....GraphMap is also used as an overlapper in a new de novo genome assembly project called Ra (h...2568 days ago
DarkHorse: a method for genome-wide prediction of horizontal gene transfer
A new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationall...2553 days ago
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Mulan: MUltiple sequence Local AligNment and conservation visualization tool
...d visualize conservation profiles for evolutionarily distant and closely related species. Input formats, automated data upload from the UCSC Genome Browser, gene annotation, ann...2525 days ago