Address of the bookmark: http://ancestralgenomes.org/

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

• January 20th, 2016 - New! Bpipe 0.9.9 released!
• Download latest, all
• Documentation
• Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

http://biogps.org/#goto=welcome

Address of the bookmark: http://biogps.org/#goto=welcome

LPI scores are inversely proportional to the phylogenetic distance between database match sequences and the query genome. These scores are useful not only for large-scalede novo predictions of horizontally transferred proteins, but can also serve as an independent quality control test for potential horizontal transfer candidates identified by alternative methods, especially those based on nucleic acid signatures. Candidates having high LPI scores are unlikely to have been horizontally transferred, since they are highly conserved among closely related organisms.

One unique and powerful feature of the DarkHorse HGT Candidate database is the opportunity to explore the phylogenetic background of potential HGT donors as well as recipients. The breadth of the database allows not only query sequences, but also their database match partners to be evaluated for sequence similarity or novelty compared to taxonomically related organisms.

DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A brief tutorial page is also available on-line.

Address of the bookmark: http://darkhorse.ucsd.edu/download.html

More at https://boards.greenhouse.io/twistbioscience/jobs/3135495?gh_src=9ecc0b941us

(1) Convert genome position from one genome assembly to another genome assembly

In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

(2) Convert dbSNP rs number from one build to another

(3) Convert both genome position and dbSNP rs number over different versions

Run:

liftOver input.bed hg18ToHg19.over.chain.gz output.bed unlifted.bed

The outformat is as follow:

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

For example:

If you liftOver chr4:6497-6497 from hg19 to GRch38 and it return "deleted in new". 

It means chr4:6497-6497 is part of a genomic contig on hg19 that is not anymore mapped on GRch38 because the new assembly is now better built without including this contig.

CSBFinder implements a novel methodology for the discovery, ranking, and taxonomic distribution analysis of colinear syntenic blocks (CSBs) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSBs in large genomic datasets. The discovered CSBs are ranked according to a probabilistic score and clustered to families according to their gene content similarity.

Address of the bookmark: https://github.com/dinasv/CSBFinder

https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html