BOL: Related items

YASRA: Reference based assembler

Abhimanyu Singh — Wed, 01 Mar 2017 08:32:45 -0600

YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a pairwise sequence aligner compatible with BLASTZ. Special scoring sets were derived to improve the performance, both in runtime and quality for 454 and Illumina sequence reads.

YASRA uses LASTZ (http://bx.psu.edu/miller_lab for released version and http://www.bx.psu.edu/~rsharris/lastz/newer for newer version) for aligning the sequences to the reference genome. Please install LASTZ (the newest version on http://www.bx.psu.edu/~rsharris/lastz/newer) and add the LASTZ binary in your executable/binary search path before installing YASRA.

Address of the bookmark: https://github.com/aakrosh/YASRA

CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R

Shruti Paniwala — Wed, 11 Nov 2020 23:06:03 -0600

CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutionary biologists working in the field of comparative genomics.

Address of the bookmark: https://gitlab.gwdg.de/mpievolbio-it/crbhits

Bioinformatics opening at ICGEB NEW DELHI

Thu, 02 Mar 2017 04:16:36 -0600

ICGEB NEW DELHI

Applications are invited for:

Junior Research Fellow, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: M.Sc. (preferably in Biotechnology, Life Sciences or Zoology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference. Bioinformatics expertise required.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Research Associate, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: Ph.D. (in Biology, Biotechnology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Multi-metagenome assembly

Radha Agarkar — Fri, 03 Mar 2017 10:14:18 -0600

This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

BLAST options, setting and defaults

Jit — Mon, 10 Dec 2018 08:29:37 -0600

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST.

A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes

	BLASTN	BLASTP	BLASTX	TBLASTN	TBLASTX	PSIBLAST
Gap opening penalty: cost to open a gap [integer]	default = 5	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 5
Gap extension penalty: cost to extend a gap [integer]	default = 2	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 2
Nucleic match: reward for a match in the BLAST portion of run [integer]	default = 1	n/a	n/a	n/a	n/a	default = 1
Nucleic mismatch: penalty for a mismatch in the blast portion of run [integer]	default = -3	n/a	n/a	n/a	n/a	default = -3
Expectation value: (E) [real]	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0
Word size: the size of the initial word that must be matched between the database and the query sequence	default = 11	default = 3	default = 3	default = 3	default = 3	default = 11
Max scores: Number of one-line descriptions (V) [Integer]	default = 25	default = 25	default = 25	default = 25	default = 25	default = 25
Max alignments: number of alignments to show (B) [integer]	default = 15	default = 15	default = 15	default = 15	default = 15	default = 15
Query filter: filter applied to the query sequence	default = DUST	default = SEG	default = SEG	default = SEG	default = SEG	default = DUST
Query genetic code: genetic code to be used in BLASTX translation of the query	n/a	n/a	default = universal	default = universal	default = universal	n/a
Matrix: substitution matrix to be used for amino acid comparisons	no default	default = blosum62	default = blosum62	default = blosum62	default = blosum62	no default

Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX

Gaps Open	Gap Extension
10	1
10	2
11	1
8	2
9	2

Address of the bookmark: https://www.arabidopsis.org/Blast/BLASToptions.jsp

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

Python vs Perl

Rahul Agarwal — Thu, 11 Jul 2013 14:39:19 -0500

Why bioinformatician still using Perl when Python is easy to code, good in ReXp and faster than perl?

Junior Research Fellow (JRF)

Sat, 13 Jul 2013 11:17:22 -0500

School of Biotechnology
Gautam Buddha University
Greater Noida, UP - 201310

Applications are invited for one position of Junior Research Fellow (JRF) in a Department of Biotechnology (DBT) sponsored research project entitled “Design, synthesis and evaluation of potent aminopeptidase inhibitors for malarial therapy” under the supervision of Dr. Shakti Sahi.

The monthly fellowship of JRF will be Rs 12,000/- plus HRA as per the University rules.

Essential Qualification: Master degree in any discipline of Life Science with NET qualified.

Desirable Qualification: Preference will be given to candidates having research experience in in silico drug designing/Bioinformatics.

Interested candidates may send their resume to undersigned on or before 14th July 2013 by post-mail/e-mail shaktis@gbu.ac.in or shaktisahi@gmail.com. No TA and DA will be paid for appearing for the interview. Dr. Shakti Sahi (Principle Investigator)

Advertisement:
www.gbu.ac.in/Recruitment/JRF_Advt_DBTProject_Shakt

gbtools: Interactive Visualization of Metagenome Bins in R

Jit — Sun, 26 Mar 2017 15:41:31 -0500

We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of annotations, including taxonomic assignments from conserved marker genes or SSU rRNA genes, can be imported simultaneously; users can choose which annotations to plot. Bins can be manually defined from plots, or be imported from third-party binning tools and overlaid onto plots, such that results from different methods can be compared side-by-side. gbtools reports summary statistics of bins including marker gene completeness, and allows the user to add or subtract bins with each other.

Tool at https://github.com/kbseah/genome-bin-tools

Address of the bookmark: http://journal.frontiersin.org/article/10.3389/fmicb.2015.01451/full

Nedelec Lab

Sat, 13 Jul 2013 17:38:55 -0500

Location :European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

Our long-term research objective is to understand microtubule organization in living cells, with an emphasis on mitosis. We develop in-vitro assays, quantitative image analysis and cytosim, a computer simulation to study cellular architecture from a mechanistic angle, modeling the interactions of microtubules and related proteins such as molecular motors. In the past, we combined simulations and experiments to study microtubule self-organization, and the mechanical stability of two interacting asters. More recently, we looked at the focusing of mitotic fibers, the formation of antiparallel arrays of microtubules in fission yeast and the spindle positionning in C. elegans.
We are supported by BioMS, an initiative in Systems Biology, and involved in Cell networks.

Link: http://www.cytosim.org