<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/41459?offset=840 https://bioinformaticsonline.com/bookmarks/view/34038/quota-synteny-alignment Mon, 31 Jul 2017 04:11:57 -0500 https://bioinformaticsonline.com/bookmarks/view/34038/quota-synteny-alignment <![CDATA[Quota synteny alignment]]> Typically in comparative genomics, we can identify anchors, chain them into syntenic blocks and interpret these blocks as derived from a common descent. However, when comparing two genomes undergone ancient genome duplications (plant genomes in particular), we have large number of blocks that are not orthologous, but are paralogous. This has forced us sometimes to use ad-hoc rules to screen these blocks. So the question is: given the expected depth (quota) along both x- and y-axis, select a subset of the anchors with maximized total score.

Address of the bookmark: https://github.com/tanghaibao/quota-alignment

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42148/chromatiblock-scalable-whole-genome-visualisation-of-structural-changes-in-prokaryotes Sat, 22 Aug 2020 05:17:18 -0500 https://bioinformaticsonline.com/bookmarks/view/42148/chromatiblock-scalable-whole-genome-visualisation-of-structural-changes-in-prokaryotes <![CDATA[chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes]]> To create a fresh environment for chromatiblock to run in do:

conda create --name chromatiblock
conda activate chromatiblock
conda install chromatiblock --channel conda-forge --channel bioconda

Then in future to run chromatiblock you can reactivate this environemtn using conda activate chromatiblock

Direct download:

Alternatively you can download and run the script from here.

Address of the bookmark: https://github.com/mjsull/chromatiblock

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