BOL: Related items

Spines

Jitendra Narayan — Tue, 09 Feb 2016 05:07:15 -0600

Spines

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

http://www.broadinstitute.org/science/programs/genome-biology/spines

Address of the bookmark: http://www.broadinstitute.org/science/programs/genome-biology/spines

Awesome bioinformatics pipelines !

Jitendra Prajapati — Wed, 30 Mar 2016 21:50:41 -0500

A curated list of awesome pipeline toolkits ...

https://github.com/pditommaso/awesome-pipeline

Address of the bookmark: https://github.com/pditommaso/awesome-pipeline

DarkHorse

Jit — Wed, 22 Jun 2016 05:37:38 -0500

DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid sequences, then using these matches to calculate a lineage probability index (LPI) score for each genome protein.

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

MEME suite

Bulbul — Fri, 23 Dec 2016 08:49:55 -0600

Motif based sequence analysis suits

The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.

The MEME Suite supports motif-based analysis of DNA, RNA and protein sequences. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (MEME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). In addition to motif discovery, the MEME Suite provides tools for scanning sequences for matches to motifs (FIMO, MAST and GLAM2Scan), scanning for clusters of motifs (MCAST), comparing motifs to known motifs (Tomtom), finding preferred spacings between motifs (SpaMo), predicting the biological roles of motifs (GOMo), measuring the positional enrichment of sequences for known motifs (CentriMo), and analyzing ChIP-seq and other large datasets (MEME-ChIP).

The MEME Suite is comprised of a collection of tools that work together, as shown below. Not all the tools are available as webservices, so to get the full power of the MEME Suite you will need to download and install a local copy of the software. To see what has changed recently you can peruse the release notes.

http://meme-suite.org/

Address of the bookmark: http://meme-suite.org/

Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes

Jit — Fri, 02 Mar 2018 04:56:23 -0600

Horizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in multicellular eukaryotes. In order for a eukaryotic species to gain a gene by HGT, foreign DNA must enter the host nucleus, integrate into the genome, and in more complex organisms it must enter the sequestered germline in order to be transmitted to offspring. Once there, it must not experience strong negative selection, despite potential for genetic incompatibility with the host genome and mismatch between the niche of the donor and the host. Over the longer term, foreign DNA may become “domesticated” in the recipient genome and provide novel function.

Following are the popular tool to detect HGT in genomes:

T-REX / 3.22

HGT detection / download & compile

20525630

RANGER-DTL / 2.0

HGT detection / download binary

22689773

PhyloNet / 3.6.1

HGT detection / download binary

18662388

Jane / 4.01

HGT detection / download binary (!license!)

20181081

TREE-PUZZLE / 5.3.rc16

HGT detection / download & compile

11934758

CONSEL / 0.20

HGT detection / download

11751242

DarkHorse / 1.5 rev170

HGT detection / download & install

17274820

HGTector / 0.2.1

HGT detection / git clone

25159222

EGID / 1.0

HGT detection / download

22355228

GeneMarkS / 4.30

HGT detection / download binary (!license!)

9461475

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.

MITObim - mitochondrial baiting and iterative mapping

Rahul Nayak — Tue, 08 May 2018 04:15:25 -0500

This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article can be found here. Kindly cite the article if you are using MITObim in your work. The pipeline was originally developed for Illumina data, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms.

Below you can find a few basic tutorials for how to run MITObim and I encorage you to give them a try with the testdata that comes with this Repo, just to make sure everything is running smoothly on your system. It'll only take a few minutes and will potentially safe you a lot of time down the line.

I provide further examples here as Jupyter notebooks. Get in touch if you feel like sharing your particular MITObim solution and I'd be happy to put it up here, too!

Address of the bookmark: https://github.com/chrishah/MITObim

vcfR: a package to manipulate and visualize VCF data in R

Jit — Thu, 25 Oct 2018 09:05:59 -0500

VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data.

Address of the bookmark: https://github.com/knausb/vcfR