Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

Address of the bookmark: http://greengenes.lbl.gov/cgi-bin/nph-index.cgi

Title of Project : 1. “Analysis Of The Structures Of Known Antimicrobial Peptides Using Machine Learning Algoitms And Molecular Dynamics Simulations”

Senior Research Fellow /1 Post

Qualification: First class M.Sc. in Bioinformatics/ Biological Sciences from recognized university with 2 years research experience and CSIR/UGC/ICMR net qualified OR First class M.Sc. in Bioinformatics/ Biological Sciences from recognized university with 2 years research experience Research experience in bioinformatics and wetlab methods.

Age: Not exceeding 35 Years

Pay Scale : Rs.18,000/- + 30% HRA Rs.14,000/- + 30% HRA

Project Assistant (Level-II) /1 Post

Qualification: First class M.Sc. in Bioinformatics/ Biological Sciences/Computer Sciences Training experience in bioinformatics and wetlab methods .

Age: Not exceeding 28 Years

Pay Scale : Rs.8,000
How to apply
Candidates must bring along with them all the relevant documents in original and one set of attested photocopies of the same and one passport size recent colour photograph.

Walk-in-Interview on 28.06.2016 between 09:00 hrs. to 12:00 hrs.

More at http://www.nirrh.res.in/links/job_oppotunities.htm

Address of the bookmark: http://biobits.org/samtools_primer.html

bcftools: a set of companion tools, currently bundled with SAMtools, for identifying and filtering genomics variants.

bowtie: widely used, open source alignment software for aligning raw sequence reads to a reference genome.

BAM Format: binary, compressed format for storing SAM data.

BCF Format: Binary call format. Binary, compressed format for storing VCF data.

CIGAR String: Compact Idiosyncratic Gapped Alignment Report. A compact string that (partially) summarizes the alignment of a raw sequence read to the reference genome. Three core abbreviations are used: M for alignment match; I for insertion; and D for Deletion. For example, a CIGAR string of 5M2I63M indicates that the first 5 base pairs of the read align to the reference, followed by 2 base pairs, which are unique to the read, and not in the reference genome, followed by an additional 63 base pairs of alignment.

FASTA Format: text format for storing raw sequence data. For example, the FASTA file at: http://www.ncbi.nlm.nih.gov/nuccore/NC_008253 contains entire genome for Escherichia coli 536.

FASTQ Format: text format for storing raw sequence data along with quality scores for each base; usually generated by sequencing machines.

genotype likelihood: the probability that a specific genotype is present in the sample of interest. Genotype likelihoods are usually expressed as a Phred-scaled probability, where P = 10 ^ (-Q/10). For example, if the genotype TT (both alleles are T) at position 1,299,132 in human chromosome 12 (reference G) is 37, this translates to a probability of 10^-37/10 = 0.0001995, meaning that there is very low probability that the reads in your sample support a TT genotype. On the other hand, a genotype of AA at the same position with a score of 0 translates into a probability of 10^-0 = 1, indicating extremely high probability that your sample contains a homozygous mutation of G to A.

mate-pair: in paired-end sequencing, both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. The two ends which are sequenced form a pair, and are frequently referred to as mate-pairs.

QNAME: unique identifier of a raw sequence read (also known as the Query Name). Used in FASTQ and SAM files.

paired-end sequencing: sequencing process where both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. Particularly useful for identifying structural rearrangements, including gene fusions.

Phred-scaled probability: a scaled value (Q) used to compactly summarize a probability, where P = 10^-Q/10. For example, a Phred Q score of 10 translates to probability (P) = 10^-10/10 = 0.1. Phred-scaled probabilities are common in next-generation sequencing, and are used to represent multiple types of quality metrics, including quality of base calls, quality of mappings, and probabilities associated with specific genotypes. The name Phred refers to the original Phred base-calling software, which first used and developed the scale.

Phred quality score: a score assigned to each base within a sequence, quantifying the probability that the base was called incorrectly. Scores use a Phred-scaled probability metric. For example, a Phred Q score of 10 translates to P=10^-10/10 = 0.1, indicating that the base has a 0.1 probability of being incorrect. Higher Phred score correspond to higher accuracy. In the FASTQ format, Phred scores are represented as single ASCII letters. For details on translating between Phred scores and ASCII values, refer to Table 1 of this useful blog post from Damian Gregory Allis.

read-length: the number of base pairs that are sequenced in an individual sequence read.

read-depth: the number of sequence reads that pile up at the same genomic location. For example, 30X read-depth coverage indicates that the genomic location is covered by 30 independent sequencing reads. Increased read-depth translates into higher confidence for calling genomic variants.

RNAME: reference genome identifier (also known as the Reference Name). Within a SAM formatted file, the RNAME identifies the reference genome where the raw read aligns.

SAM Flag: a single integer value (e.g. 16), which encodes multiple elements of meta-data regarding a read and its alignment. Elements include: whether the read is one part of a paired-end read, whether the read aligns to the genome, and whether the read aligns to the forward or reverse strand of the genome. A useful online utility decodes a single SAM flag value into plain English.

SAM Format: Text file format for storing sequence alignments against a reference genome. See also BAM Format.

SAMtools: widely used, open source command line tool for manipulating SAM/BAM files. Includes options for converting, sorting, indexing and viewing SAM/BAM files. The SAMtools distribution also includes bcftools, a set of command line tools for identifying and filtering genomics variants. Created by Heng Li, currently of the Broad Institute.

single-read sequencing: sequencing process where only one end of a DNA or RNA fragment is sequenced. Contrast with paired-end sequencing.

VCF Format: Variant call format. Text file format for storing genomic variants, including single nucleotide polymorphisms, insertions, deletions and structural rearrangements. See also BCF format.

NextGenerationSequencing
A high-throughput sequencing method which parallelizes the sequencing process, producing thousands or millions of sequences at once.

DeepSequencing
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced.

Paired-EndSequencing
Sequence both ends of the same fragment and keep track of the paired data.

Adapter
Short oligonucleotides which are attached to the DNA to be sequenced. An adapter can provide a priming site for both amplification and sequencing of the adjoining, unknown nucleic acid.

Library
A collection of DNA fragments with adapters ligated to each end.

BridgeAmplification
Generation of in situ copies of a specific DNA molecule on an oligo-decorated solid support.

EmulsionPCR
A method for bead-based amplification of a library. A single adapter-bound fragment is attached to the surface of a bead, and an oil emulsion containing necessary amplification reagents is formed around the bead/fragment component. Parallel amplification of millions of beads with millions of single strand fragments produces a sequencer-ready library.

Alignment
Mapping of sequence reads to a known reference sequence

Referencesequence/genome 
A fully assembled version of a genome that can be used for mapping short DNA sequence reads for comparisons of genomes from various individuals

CoverageDepth
The number of nucleotides from reads that are mapped to a given position of reference genome.

Specificity 
The percentage of sequences that map to the intended targets out of total bases per run.

Uniformity 
The variability in sequence coverage across target regions.

Homopolymer
Uninterrupted stretch of a single nucleotide type (e.g., TTT or GGGGGG)

InDel
InDel stands for Insertion or deletion. A form of structural variation in which a DNA segment is either deleted or inserted.

SNP 

SNP stands for Single Nucleotide Polymorphism. A single base difference found when comparing the same DNA sequence from two different individuals.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

• BLAST Tool: added support for local custom BLAST databases
• Graphical Sequence View: added log scaling option for graph tracks
• Generic Table View: new tutorial added

Bug Fixes and Improvements

• Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
• Tree View: layout updated to better accommodate nodes of different sizes
• Table Import Dialog (MacOS): fixed issue with table visibility
• Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
• Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
• Graphical Sequence View: fixed protein coloration methods
• Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
• Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
• Search View: ORF Finder – fixed incorrect protein lengths
• Fixed bug with not opening project file (.gbp) on a click
• Fixed issues in GVF import
• Fixed BLAST Search tool against NCBI databases not working
• Fixed tblastn (protein BLAST) not working in standalone mode
• Fixed GTF export failure

Applications are invited for a post in DST, India funded Project entitled: "Positive and negative impacts of macromolecular crowding agents during target site location by DNA binding proteins – origin of optimal search at physiological ionic concentration (Reference Number: ECR/2016/000188) ''. The selected candidate will be appointed purely on temporary basis, initially for two years as a JRF that may be extended to one year of SRF based on the performance.

Position: Junior Research Fellow (1)

Qualifications & Experience: Candidate must have a consistently good academic record with at least 60% marks in all throughout and must have qualified NET/GATE.

Desirable: Basic knowledge in the field of biophysics, molecular simulations and computational biology are desirable.

Salary: Consolidated Rs. 25,000 per month.

Tenure: The project duration is for three years and the selected candidate would be appointed after an interview. Appointment will be purely on temporary basis as stipulated by the existing rules of the University.

Interested candidates need to send an application to the address mentioned below mentioning the name of the project and post applied for (on the cover of the envelope).

The applications along with CV should be mailed at the address given below. Name, address, contact number and e. mail address of two referees must be enclosed with the application. The last date for the application is July 31st 2016.

Dr. Arnab Bhattacharjee (Principal Investigator)
Assistant Professor
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
E-mail: arnab@jnu.ac.in

Note: 1. Only shortlisted candidates will be communicated to appear in the interview at SCIS, JNU and no other communications in this regard will be entertained.

2. No TA/DA will be paid for appearing in interview.

More at http://ird.iitd.ac.in/sites/default/files/jobs/project/IITD-IRD-093-2016.pdf