BOL: Related items

MCAT: Motif Combining and Association Tool

Neel — Sun, 13 Jan 2019 06:27:28 -0600

This is a pipeline for finding motifs in fasta files.
It can be run from the command line as follows:

usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C]
[-s S] [-d] [-ff] [-v V]
positive_seq negative_seq

positional arguments:
positive_seq the fasta file for the positive sequences
negative_seq the fasta file for the negative sequences

Address of the bookmark: https://github.com/yanshen43/MCAT

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Thu, 14 May 2020 15:13:30 -0500

gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/

Address of the bookmark: https://github.com/kammoji/gapFinisher

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

BioStar — Mon, 17 Aug 2020 05:25:10 -0500

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
Co-assembly of a large number of metagenomes via merging of individual metagenomes
Includes binning and bin checking, for retrieving individual genomes
The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

JUDI: Just Do It

Jit — Mon, 06 Sep 2021 02:44:35 -0500

judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings.

https://github.com/ncbi/JUDI

Address of the bookmark: https://github.com/ncbi/JUDI

iMAGine - in silico MetAGenomics pipeline

BioStar — Sat, 06 Jul 2024 04:32:18 -0500

iMAGine is a metagenomic workflow which includes filtering, assembling, and binning.

This workflow includes the following tools which are needed to be installed in the system.

Address of the bookmark: https://github.com/avishekdutta14/iMAGine

List of GOI approved peer reviewed bioinformatics and computational biology journals

Jit — Tue, 25 Apr 2017 05:03:27 -0500

Unfortunately, we now live in a world where the integrity of peer-reviewed journals is being threatened by the rise of the academic version of fake news – something many call “predatory publishing". Mostly in academic publishing world, "predatory open access publishing" is an exploitative open-access publishing business model that involves charging publication fees to authors without providing the editorial and publishing services associated with legitimate journals (open access or not).

Nearly 20% of the such journals have a flashy impact factor and quick publication time, which are quick give-aways. Interestingly, under contact address, some journal websites do not even provide any address to contact. All of this has led to the emergence of a new and dark market of deceptive publishers that exploit the concept of open access and provide channels for “scientific journal” publication with little or no peer review. For a fee, they will publish almost anything – even if the study was fatally flawed. And these journals provide a forum that can be used as a channel to publish fraudulent “advocacy research.” You can find list of certain such publishers at "Beall's List" http://beallslist.weebly.com/

Keeping all these in mind, Government of India (GOI) decided to approved certain bioinformatics and computational biology journals for your research publication.

Following are the list of GOI validated and peer reviewed bioinformatics and computational biology journals:

NOTE:Each journal details are in following order Tittle\nSource\nSubject.
Point to remember: The list of journals are NOT sorted in any ascending or descending order.

If I missed any other GOI validated bioinformatics journal, then please report me in comment section.

Open Bioinformatics Journal
Scopus
Computer Science; Engineering; Medicine

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
WoS
BIOLOGY & BIOCHEMISTRY

Advances and Applications in Bioinformatics and Chemistry
Scopus
Biochemistry, Genetics and Molecular Biology Chemistry; Computer Science

Advances in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Engineering

Applied Bioinformatics
Scopus
Agricultural and Biological Sciences; Computer Science

BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Bioinformatics and Biology Insights
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science; Mathematics

BMC BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

BRIEFINGS IN BIOINFORMATICS
WoS & Scopus
COMPUTER SCIENCE

Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference
Scopus
Medicine

Current Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Current Protocols in Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology

JOURNAL OF COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS
ICI
BIOLOGICAL SCIENCE

Journal of integrative bioinformatics
Scopus
Medicine

Journal of Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Mathematical Biology and Bioinformatics
Scopus
Engineering; Mathematics

Trends in Bioinfprmatics
Scopus
Computer Science

Eurasip Journal on Bioinformatics and Systems Biology
Scopus
General; Computer Science; Mathematics; Medicine

Evolutionary Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

Genomics, Proteomics and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Mathematics

IEEE-ACM Transactions on Computational Biology and Bioinformatics
WoS
COMPUTER SCIENCE

International Journal of Bioinformatics Research and Application
Scopus
Biochemistry, Genetics and Molecular Biology; Medicine, Health

International Journal o f Data M ining and Bioinformatics
WoS & Scopus
COMPUTER SCIENCE

IPSJ Transactions on Bioinformatics
Scopus
Biochemistry, Genetics and Molecular Biology;Computer Science

Journal of Bioinformatics and Computational Biology
WoS & Scopus
COMPUTER SCIENCE

Journal of Clinical Bioinformatics
Scopus
Medicine

PLoS Computational Biology
WoS & Scopus
BIOLOGY & BIOCHEMISTRY

Reviews in Computational Chemistry
WoS & Scopus
CHEMISTRY

RSC Theoretical and Computational Chemistry Series
Scopus
Chemistry; Computer Science

Annual Reports in Computational Chemistry
Scopus
Chemistry; Mathematics

Computational and Structural Biotechnology Journal
Scopus
Biochemistry, Genetics and Molecular Biology; Computer Science

Computational and Theoretical Chemistry
WoS & Scopus
CHEMISTRY

COMPUTATIONAL BIOLOGY AND CHEMISTRY
WoS & Scopus
COMPUTER SCIENCE

COMPUTATIONAL CHEMISTRY
WoS
CHEMISTRY

Journal of Theoretical and Computational Chemistry
Scopus
Chemistry; Computer Science

Theoretical and Computational Chemistry
Scopus
Chemistry

Wiley Interdisciplinary Reviews: Computational Molecular Science
Scopus
Biochemistry, Genetics and Molecular Biology;Chemistry; Computer Science; Materials Science; Mathematics

Wiley Interdisciplinary Reviews- Computational Molecular Science
WoS
CHEMISTRY

Interdisciplinary sciences, computational life sciences
Scopus
Medicine

Interdisciplinary Sciences-Computational Life Science
WoS
Biology and Biochemistry

International Journal of Computational Biology and Drug Design
Scopus
Computer Science; Pharmacology, Toxicology and Pharmaceutics

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

NCBI Remap

Jit — Thu, 11 Feb 2016 11:02:26 -0600

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

AnnotationSketch

Jit — Sun, 25 Jun 2017 17:54:22 -0500

The AnnotationSketch module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to the Lua, Python and Rubyprogramming languages are provided.

http://genometools.org/annotationsketch.html

Address of the bookmark: http://genometools.org/annotationsketch.html