BOL: Related items

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

Jit — Mon, 18 Feb 2019 04:21:50 -0600

MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.

For further details about the underlying algorithm see the original publication:
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
Vincent Ranwez, Sébastien Harispe, Frédéric Delsuc, Emmanuel JP Douzery
PLoS One 2011, 6(9): e22594.

Address of the bookmark: https://bioweb.supagro.inra.fr/macse/index.php?menu=releases

Ideoplot

Shruti Paniwala — Mon, 13 Feb 2017 09:47:32 -0600

Simple ideogram plotting and annotation in R.

Basic usage:

Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf
-or-
Rscript Ideoplot.R --annotate annotations.bed

Options
  --ideobed, i      A bed file of reference contig lengths/chromosome names
  --heatmap, -h     Fill chromosomes with normalized heatmap
                   (described below)
  --annotate, -a    Add character annotations.
  --out, -o         PDF output name.
  --stripes, -s     Specify a file containing the layout of the
                    annotations (description below)
  --bars, -b        Add track annotations
  --reference, -f   Either hg19, or hg38
  --topdown, r      Flag, when set, flips the orientation (P arms
                    drawn on top).

Address of the bookmark: https://github.com/mchaisso/Ideoplot

Elastic BLAST !

Abhi — Tue, 06 Sep 2022 18:14:57 -0500

ElasticBLAST is a new way to BLAST large numbers of queries, faster and on the cloud. Here are the top three reasons you should use ElasticBLAST:

1. ElasticBLAST can handle much LARGER queries!

ElasticBLAST can search query sets that have hundreds to millions of sequences and against BLAST databases of all sizes.

2. ElasticBLAST is FASTER

ElasticBLAST distributes your searches across multiple cloud instances to process them simultaneously. The ability to scale resources in this way allows you to process large numbers of queries in a shorter time than you could with BLAST+.

3. ElasticBLAST is EASY to run on the cloud

ElasticBLAST is easy to set up using our step-by-step instructions (Amazon Web Services (AWS), Google Cloud Platform (GCP)) and allows you to leverage the power of the cloud. Once configured, it manages the software and database installation, handles partitioning of the BLAST workload among the various instances, and deallocates cloud resources when the searches are done.

ElasticBLAST also selects the instance (i.e., machine) type for you based on database size. Of course, you can also choose the instance type manually if you prefer.

Address of the bookmark: https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/

Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation

Jit — Tue, 16 Mar 2021 05:45:44 -0500

We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have reduced computation cost forlocal alignment , while achieving accuracy comparable to existingdefacto standard BWA-MEM tool.

https://prakharg24.github.io/papers/401851.full.pdf

Address of the bookmark: https://prakharg24.github.io/papers/401851.full.pdf

Postdoctoral Research Position in Bioinformatics in Milan

Thu, 20 Apr 2017 12:53:12 -0500

The lab of Immunobiology of Neurological Disorders has a main interest in the biological processes associated with multiple sclerosis, an inflammatory disorder of the central nervous system. The projects of interest for this application involve research on translational bioinformatics in complex human neurological disorders.

You have a PhD in Computational Science, Bioinformatics, or equivalent, and expertise in analysis and modeling of human RNA-seq data, statistics, data mining and machine learning. Excellent communication skills in English (written and oral) is a must. Flexibility and willingness to work across multiple projects and technologies in a rapidly evolving scientific context is required.
Salary will depend on qualification and experience. Starting date: immediate.

Interested candidates should send to farina.cinthia@hsr.it:

1. CV (please show evidences of relevant titles, projects, courses, references, etc.)
2. One page with a list of research topics (i.e. ongoing projects)
3. earliest availability

4. 2-3 contact names

Harvest: a suite of core-genome alignment and visualization tools

Jit — Fri, 08 Dec 2017 07:16:03 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/

FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads

Jit — Mon, 27 Feb 2017 09:49:45 -0600

FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.

Address of the bookmark: http://kakitone.github.io/finishingTool/

xmatchview: smith-waterman alignment visualization

Rahul Nayak — Thu, 28 Dec 2017 09:00:58 -0600

xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994) http://www.phrap.org) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.

http://www.bcgsc.ca/platform/bioinfo/software/xmatchview

Address of the bookmark: https://github.com/warrenlr/xmatchview

Bioinformatics walk-in-interview at Tezpur University

Thu, 02 Mar 2017 04:24:46 -0600

A walk-in-interview will be held on 09 March, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University for one (01) temporary position of Junior Research Fellow (JRF) in the DBT, Govt. of India sponsored project entitled “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics” under Dr. Siddhartha Sankar Satapathy (ssankar@tezu.ernet.in), Associate Professor, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

Essential qualification: M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET.

Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science.

Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

Remuneration: Rs. 25,000/- (Rupees twenty five thousand) only + HRA as admissible per month for the 1st two years and Rs. 28,000/- (Rupees twenty eight thousand) only + HRA as admissible per month for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- (Rupees twelve thousand) only + HRA as admissible per month for the 1st two years and Rs. 14,000/- (Rupees fourteen thousand) only + HRA as admissible per month for the 3 rd year for SRF, for the candidate without NET/GATE/BET qualification. HRA will not be provided if campus accommodation is availed.

Age: Candidate shall not be more than 28 years of age on the date of interview. Upper age limit may be relaxed up to 5 years in the case of candidate belonging to SC/ST/ OBC/Women/Differently abled.

Duration: Three (03) years or till completion of the project or until further order, whichever is earlier.

N.B. No TA/DA will be paid to the candidates for attending the interview. For further details please contact: Dr. S. S. Satapathy Associate Professor Department of Computer Science and Engineering Tezpur University, Napaam-784028 Email: ssankar@tezu.ernet.in Contact no.: +91-9435979648

More Info: www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-188-A.pdf

minialign: fast and accurate alignment tool for PacBio and Nanopore long reads

Jit — Thu, 24 May 2018 08:33:26 -0500

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.

Address of the bookmark: https://github.com/ocxtal/minialign