BOL: Related items

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

IgBLAST 1.17 is now available with improved identification of productive V gene sequences

Jit — Sun, 01 Nov 2020 16:52:58 -0600

A new release of IgBLAST (1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the web and from the FTP site. The updated package is better at identifying productive V gene sequences. We added a new field , “V frame shift”, to the IgBLAST output to indicate whether the V gene translation frame contains a frame-shift. We have also updated the definition of a productive V(D)J sequence to now exclude those with internal frame shifts.

See the new IgBLAST manual on the NCBI GitHub site for more information on setting up and running IgBLAST.

If you have any questions or concerns, please email us at blast-help@ncbi.nlm.nih.gov

Steps to find palindrome in genomes !

BioStar — Thu, 09 Mar 2023 02:56:54 -0600

Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:

Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.
Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.
Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.
Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.
Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.

Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.

Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences

Neel — Thu, 14 Aug 2025 04:02:05 -0500

Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.

The performance of the Jaeger workflow can be significantly increased by utilizing GPUs. To enable GPU support, the CUDA Toolkit and cuDNN library must be accessible to conda.

# setup bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# create conda environment and install jaeger
mamba create -n jaeger -c nvidia -c conda-forge cuda-nvcc "python>=3.9,<3.12" pip jaeger-bio


# activate environment
conda activate jaeger

Address of the bookmark: https://github.com/MGXlab/Jaeger

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations

Neel — Thu, 19 May 2022 04:29:05 -0500

The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2

Address of the bookmark: https://github.com/HuffordLab/GenomeQC

SRF Vacancy at NIPGR

Tue, 25 Mar 2014 19:20:44 -0500

Applications are invited from suitable candidates for filling up the purely temporary position of one Senior Research Fellow in DST’s Indo-Australian Joint project (with ICRISAT) entitled “Genomic Approach for Stress Tolerant Chickpea” under the guidance of Dr. Mukesh Jain, Scientist, NIPGR.

(A) Senior Research Fellow (One Post): Emoluments as per DST/DBT norms.

Candidates having M.Sc. degree (with minimum of 55% marks) or equivalent in Life Sciences/Biotechnology/Bioinformatics/ Molecular Biology or any other related field with minimum of two years of post M.Sc. research experience are eligible to apply. The candidate having computer skill (Linux, Perl, Java, MySQL) and/or experience in advanced molecular biology, next generation sequencing data analysis and molecular markers analysis will be preferred.

The position is completely on temporary basis and co-terminus with the project. The initial appointment will be for one year, which can be curtailed/extended on the basis of assessment of the candidate’s performance and discretion of the Competent Authority. NIPGR reserves the right to select the candidate against the above posts depending upon the qualifications and experience of the candidates. Reservation of posts shall be as per Govt. of India norms.

Eligible candidates may apply by sending hard copy of completed application in the given format with a cover letter showing interest and attested copies of the certificates and proof of research experience. The applications should reach at the address given below within 15 days from the date of the advertisement. The subject line on envelope must be superscribed by “Application for the Post of SRF in DST - AISRF project”.

Note: ONLY hard copy of the application in the given format will be accepted.

Last date April 03, 2014

Dr. Mukesh Jain
Staff Scientist
National Institute of Plant Genome Research
Aruna Asaf Ali Marg, P.O. Box NO. 10531,
New Delhi - 110067

Advertisement: http://www.nipgr.res.in/careers/vacancies_latest.php#

Genomic Basis of Evolutionary Innovations (GEvol)

BioStar — Sat, 06 Dec 2025 06:11:00 -0600

The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: „Genomic Basis of Evolutionary Innovations (GEvol)“

GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one goal: to characterise the dynamics and mechanisms of genomic innovations underlying novel traits using comparative evolutionary genomics (and related data).
Thus, projects participating in GEvol we will ask fundamental evolutionary questions such as:
1. At what level is evolution repeatable?
2. How does genomic plasticity interfere with phenotypic plasticity during evolution?
3. How do inter- and intra-specific interactions influence genomic architectures?
4. How predictable is phenotypic variation given some knowledge about the dynamics and mechanisms of underlying genome evolution?

Address of the bookmark: https://g-evol.uni-muenster.de/open-positions/

Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence

Jit — Thu, 23 Nov 2017 08:37:15 -0600

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

Address of the bookmark: https://sourceforge.net/projects/taxoblast/files/

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

Neel — Tue, 12 Jun 2018 13:17:13 -0500

RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes at one run and generates concise comparison of enzyme(s) performance across the genomes. For more information, please see the academic paper published online (http://www.sciencedirect.com/science/article/pii/S071734581630001X).

Address of the bookmark: https://github.com/JINPENG-WANG/RestrictionDigest