BOL: Related items

Collection of Graph Visualization tools !

Neel — Wed, 25 Jan 2023 02:57:42 -0600

Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation and sequence are separated.

https://fungidb.org/fungidb/app/downloads/Current_Release/GultimumBR650/

Address of the bookmark: https://pangenome.github.io/

Introduction to programming. Write short programs that generate graphics and animation.

Ram Yash Pal — Thu, 14 Aug 2014 23:29:04 -0500

Introduction to programming. Write short programs that generate graphics and animation.

http://funprogramming.org/

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

Charpak exchange program

Fri, 10 Nov 2023 02:33:38 -0600

The scholarship is designed for Indian students from all fields and streams of study, enrolled in an Indian institution at the Bachelors or Master’s degree level, who wish to undertake a study exchange semester programme in France (for a period of one to six months).

BENEFITS
The Charpak exchange program offers the following benefits to the awardees based on merit: monthly stipend of 860 euros social security student visa and Campus France fee waiver assistance in finding an affordable student accommodation (subject to availability)

https://www.inde.campusfrance.org/charpak-exchange-scholarship-spring-session-jan-june

MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times

Poonam Mahapatra — Sat, 02 Jun 2018 07:40:06 -0500

MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy example modified from dataset of Inoue et al. (2010). Here we conduct a commonly used time estimation method, "Approximate Likelihood Method", for the datasets including more than 10 species.

Address of the bookmark: http://www.fish-evol.com/mcmctreeExampleVert6/text1Eng.html

CroCo: A program to detect potential cross contaminations in HTS assembled transcriptomes using expression level quantification

Jit — Mon, 07 Jan 2019 18:17:44 -0600

CroCo is a program to detect cross contamination events in assembled transcriptomes using sequencing reads to determine the true origin of every transcripts.
Such cross contaminations can be expected if several RNA-Seq experiments were prepared during the same period at the same lab, or by the same people, or if they were processed or sequenced by the same sequencing service facility.
Our approach first determines a subset of transcripts that are suspiciously similar across samples using a pairwise BLAST procedure. CroCo then combine all transcriptomes into a metatranscriptome and quantifies the "expression level" of all transcripts successively using every sample read data (e.g. several species sequenced by the same lab for a particular study) while allowing read multi-mappings.
Several mapping tools implemented in CroCo can be used to estimate expression level (default is RapMap).
This information is then used to categorize each transcript in the following 5 categories :

clean: the transcript origin is from the focal sample.

cross contamination: the transcript origin is from an alien sample of the same experiment.

dubious: expression levels are too close between focal and alien samples to determine the true origin of the transcript.

low coverage: expression levels are too low in all samples, thus hampering our procedure (which relies on differential expression) to confidently assign it to any category.

over expressed: expression levels are very high in at least 3 samples and CroCo will not try to categorize it. Indeed, such a pattern does not correspond to expectations for cross contaminations, but often reflect highly conserved genes such as ribosomal gene, or external contamination shared by several samples (e.g. Escherichia coli contaminations).

Address of the bookmark: https://gitlab.mbb.univ-montp2.fr/mbb/CroCo

Gooey: Turn (almost) any Python command line program into a full GUI application with one line

BioStar — Fri, 01 Nov 2019 00:29:27 -0500

Turn (almost) any Python command line program into a full GUI application with one line

The easiest way to install Gooey is via pip

pip install Gooey

Alternatively, you can install Gooey by cloning the project to your local directory

git clone https://github.com/chriskiehl/Gooey.git

run setup.py

python setup.py install

Address of the bookmark: https://github.com/chriskiehl/Gooey

BLAST+ updated !!!

Jit — Tue, 16 Jun 2015 16:55:24 -0500

A new version (2.2.31) of the stand-alone BLAST executables (Linux, Windows and MacOSX on FTP) is now available. New features include support for BLAST-XML2 specification (information here) and JSON BLAST output format, as well as several bug fixes and improvements. The BLAST AMI at AWS will also be updated to 2.2.31 (see this BLAST Help page for more information). For a full list of improvements, see the release notes.

More at http://www.ncbi.nlm.nih.gov/news/06-16-2015-blast-plus-update/?