BOL: Related items

NCBIBLAST+ 2.14.1 now available

Neel — Wed, 30 Aug 2023 02:36:13 -0500

#NCBIBLAST+ 2.14.1 now available with improved documentation, faster and more reliable database downloads, and some bug fixes.

Check out the changes they made.

They added the cleanup-blastdb-volumes.py script to remove unused BLAST database volumes. Read the documentation here.

They also switched the protocol from ftp to https to access BLAST databases for increased performance and reliability when downloading data from the NCBI with the update_blastdb.pl script.

And fixed a few bugs related to downloading data from the NCBI, and mt_mode crashing blastn and blastx.

Check out the release notes.

Download BLAST+ 2.14.1

Questions or comments? Please write the BLAST help desk.

More info and download: https://blast.ncbi.nlm.nih.gov/doc/blast-news/2023-BLAST-News.html

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/

Bioinformatics National Certification (BINC) Examination 2016

Wed, 11 May 2016 02:17:44 -0500

Bioinformatics National Certification (BINC) Examination 2016

Department of Biotechnology, Government of India, New Delhi & Pondicherry University, Puducherry

Starting of online submission of application : April 13, 2016

Last date for submission of application : May 13, 2016

Examination consists of two parts:

Part - I (Paper - I) : June 12, 2016 (10 AM -12 PM)
Part - II (Paper • II & III) : June 26, 2016 (9 AM • 12 PM & 2 PM • 4 PM)

Objective: Pondicherry University, on behalf of the Department of Biotechnology (DBT),
Government of India, will conduct the Bioinformatics National Certification (BING) examination. The objective of this examination is to identify Bioinformatics professionals
for further studies as well as to help potential employers in recruitment of candidates having exceptionally good Bioinformatics skills.

Eligibility : Bachelor degree in Life Sciences, Physical Sciences, Chemical Sciences, Mathematical Sciences, Agriculture, Veterinary, Medicine, Pharmacy, Engineering and Technology are eligible to appear for the examination. They need not have any formal training, diploma or certificate in Bioinformatics.

Application and syllabus : The online application can be filled from April 13, 2016 to May 13, 2016.

Syllabus for the examination is available online.

It consists of five sections:
Bioinformatics, Biology, Physical and Chemical Sciences, Mathematics & Statistics and Computer Science & Information Technology.

Examination : The examination fee is Rs. 600/- for general candidates, Rs. 400/- for women/OBC candidates and Rs. 200 for SC/ST candidates, and no fee for physically challenged candidates.

The online Part - I (Paper - I) examination is scheduled on June 12,2016 and Part- II (Paper - II and Paper- III) on June 26, 2016. The Paper- I will be of objective type and candidates scoring a minimum of 40% marks in Paper - I will be called to appear in Part II examination.

Part II examination consists of two papers : The Paper - II will be of short answer type questions of three hours duration while the Paper- III will be a practical examination of two hours duration to test analytical ability and programming skill of candidates.

Research Fellowships for all the successful candidates those who are interested and qualified in pursuing Ph.D. in India will be awarded. In addition, cash prizes will be awarded to the top 10 successful candidates.

The details of examination centres, other details and submission of application, please
visit: http://www.pondiuni.edu.in/exams/binc/

Ancestral sequence reconstruction steps !

Surabhi Chaudhary — Fri, 18 May 2018 08:28:26 -0500

Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an ancestral gene and expression of the corresponding ancestral protein. The idea of protein 'resurrection' was suggested in 1963 by Pauling and Zuckerkandl. Some early efforts were made in the eighties-nineties, led by the laboratory of Steven A. Benner, showing the potential of this technique – one that only started to be fulfilled in the post-genomic era. Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of a greater variety of and much more ancient genes. Over the last decade, ancestral protein resurrection has developed as a strategy to reveal the mechanisms and dynamics of protein evolution.

BEAST is the best way to predict the ancestral structure. but, I suggest following steps?

1- Alignments "Mafft - http://mafft.cbrc.jp/alignment/software/source.html"

mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_Alig.fasta

2- Your dataset has a good phylogenetic signal, is possible to perform with Tree-Puzzle "http://www.tree-puzzle.de";

3 - This dataset which the saturation index, I perform with "http://dambe.bio.uottawa.ca/dambe.asp";

4- Has evidence of possible recombination in your dataset, the evaluate if this presence or absence, because this may to influence the grouping of clades, I perform with

---recombination

4.1- Phi-test, implemented in SplitTree4"http://www.splitstree.org", (.nex file)

4.2- GARD deployed in webserver in the DataMonkey "http://www.datamonkey.org/" - turning to the amino acid seaview -> view proteins -> save as ...) Ideally do a tree-based groups.

4.3- RDP4 for download and installation on Windows in "http://web.cbio.uct.ac.za/~darren/rdp.html"

4.4- Hyphy (Mac, Windows, Linux) in "http://hyphy.org/w/index.php/Download"

4.5- Path-o-Gen (temporal structure of a tree input file -> arquivo.tre)

These steps above, I call of pre-processing to inferences phylogenetic...

5- Perform phylogenetic tree, used Bayesian Inference with Molecular Clock, but is necessary Clock Testing:

- This step is performed with program Beast (Beauti, Beast and TreeAnnotator), and Tracer_v1.5 more FigTree to inspection.

- Tutorials: http://beast.bio.ed.ac.uk/tutorials

- Downloads: http://beast.bio.ed.ac.uk/downloads

BINC 2016

Jit — Wed, 11 May 2016 07:15:03 -0500

Bioinformatics National Certification (BINC) Examination 2016

Department of Biotechnology, Government of India, New Delhi & Pondicherry University, Puducherry

Starting of online submission of application : April 13, 2016

Last date for submission of application : May 13, 2016

Examination consists of two parts:

Part - I (Paper - I) : June 12, 2016 (10 AM -12 PM)
Part - II (Paper • II & III) : June 26, 2016 (9 AM • 12 PM & 2 PM • 4 PM)

Application and syllabus : The online application can be filled from April 13, 2016 to May 13, 2016.

Syllabus for the examination is available online.

It consists of five sections:
Bioinformatics, Biology, Physical and Chemical Sciences, Mathematics & Statistics and Computer Science & Information Technology.

Examination : The examination fee is Rs. 600/- for general candidates, Rs. 400/- for women/OBC candidates and Rs. 200 for SC/ST candidates, and no fee for physically challenged candidates.

The details of examination centres, other details and submission of application, please
visit: http://www.pondiuni.edu.in/exams/binc/

MSAProbs - Parallel and accurate multiple sequence alignment

Neel — Tue, 09 Jul 2019 23:58:44 -0500

MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. In addition, MSAProbs is optimized for shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory systems using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.

Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

Do you think it's important for everyone to pass BINC exam?

Jit — Wed, 11 May 2016 07:25:34 -0500

The Department of Biotechnology (DBT), Government of India has instituted BINC examination with the objective of evaluating the Bioinformatics knowledge & skills of students. Do you think it is important ?

Shouji: a fast and efficient pre-alignment filter for sequence alignment

Jit — Mon, 04 Nov 2019 07:09:45 -0600

The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes.

We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator design that adopts modern FPGA (field-programmable gate array) architectures to further boost the performance of our algorithm.

More at https://github.com/CMU-SAFARI/Shouji

Address of the bookmark: https://github.com/CMU-SAFARI/Shouji

Sample BINC question paper 2016 - part1

Radha Agarkar — Fri, 13 May 2016 03:41:48 -0500

Please download the sample bioinformatics question paper for BINC 2016

CLARK: Fast, accurate and versatile sequence classification system

Jit — Sat, 15 Feb 2020 01:49:01 -0600

CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/