BOL: Related items

Heatmapper: web-enabled heat mapping for all

Jit — Mon, 01 Oct 2018 08:34:41 -0500

Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. Heatmapper allows users to generate, cluster and visualize:

1) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; 2) pairwise distance maps;

3) correlation maps;

4) image overlay heat maps;

5) latitude and longitude heat maps and

6) geopolitical (choropleth) heat maps.

Heatmapper offers a number of simple and intuitive customization options for easy adjustments to each heat map’s appearance and plotting parameters. Heatmapper also allows users to interactively explore their numeric data values by hovering their cursor over each heat map, or by using a searchable/sortable data table view.

Ref https://www.ncbi.nlm.nih.gov/pubmed/27190236

Address of the bookmark: http://www2.heatmapper.ca/

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

HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads

Rahul Nayak — Tue, 08 May 2018 04:27:22 -0500

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

BioStar — Fri, 21 Sep 2018 10:19:52 -0500

Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:

sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config

On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:

sudo fink install bzip2-dev pkgconfig

Address of the bookmark: https://github.com/neufeld/pandaseq

LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.

Neel — Sun, 13 Jan 2019 07:05:53 -0600

LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.

The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE, http://www.expasy.org/prosite/) to locate cores of important enzymes if they occur.

Address of the bookmark: https://github.com/xzhub/LTR_Finder

chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Jit — Mon, 23 Mar 2020 06:20:04 -0500

Python package to detect chromatin loops (and other patterns) in Hi-C contact maps.

Stable version with pip:

pip3 install --user chromosight

Stable version with conda:

conda install -c bioconda -c conda-forge chromosight

or, if you want to get the latest development version:

pip3 install --user -e git+https://github.com/koszullab/chromosight.git@master#egg=chromosight

Address of the bookmark: https://github.com/koszullab/Chromosight

Protein-Protein Interaction Sites Predictions !

Poonam Mahapatra — Wed, 25 Apr 2018 04:53:20 -0500

The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues participating in a given PPI. Information about a protein’s interaction partners allows scientists to construct protein interaction networks, such as signaling pathways, which in turn facilitate the understanding of many biological and clinical observations.

Following are the list of tools commonly used to PPIs predictions:

Protein-Protein Interaction Sites

PPISP

A consensus neural network method for predicting protein-protein interaction sites

HOMCOS

A server to predict interacting protein pairs and interacting sites by homology modeling of complex structures

HotPOINT

Prediction of protein interfaces using an empirical model

ISIS

Prediction of interaction hotspots from sequence

KFC server

Automated decision-tree approach to predicting protein-protein interaction hot spots

meta-PPISP

A meta server for predicting protein-protein interaction sites. meta-PPISP is built on three individual web servers: cons-PPISP, PINUP, and Promate

ODA

Identification of optimal surface patches with the lowest docking desolvation energy values

PINUP

Protein binding site prediction with an empirical scoring function

Other Sites (DNA, RNA, Metals)

CHED

Web server for predicting soft metal binding sites in proteins

DBD-Hunter

A knowledge-based method for the prediction of DNA-protein interactions

DISPLAR

Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA using neural network method

iDBPs

Predicts DNA binding proteins for proteins with known 3D structure.

PFplus

A tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites

Neel — Mon, 05 Nov 2018 08:12:45 -0600

An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Address of the bookmark: https://github.com/olarerin/metaPlotR