Bio Saga Blog - A Chronicle of Life Sciences & Informatics

3 Days National Level Workshop on "NGS Data Analysis:Variant Calling,RNASEQ,CHIPSEQ"' 8th to 10th March 2019 09:30 AM - 05:00 PM Topics Covered ▪ Introduction to Bioinformatics ▪ Data curation using Biological databases ▪ Understanding the concept of Gene Expression & Genome Editing ▪ Gene Finding Tools ▪ Introduction to Next Generation Sequencing ▪ Searching for SRA Data for genomic samples ▪ Introduction to Sequence alignment, BLAST ▪ Variant Calling to detect mutations ▪ RNA sample studies for gene expression ▪ Introduction to ChIP-Seq technology Our 3 days comprehensive Workshop on Next Generation Sequencing Data Analysis,Variant Calling, RNAseq, ChIPseq : A Practical Introduction aims at providing systematic Hands-on-Training on using Data Analysis application/tools for the NGS data. This workshop had been conceptualized by eminent scientist having substantial experience in the field of Data Analysis. ...

At the Bio-IT World Conference last week, Intel unveiled a new website, dubbed Optimized Code, that offers access to versions of several popular open-source bioinformatics analysis tools that the company has optimized to run on Intel Xeon processors, with the aim of generating results faster and more efficiently than standard iterations of these solutions. The first set of applications that the company has released specifically for genomic analysis include optimized versions of  the Broad Institute's Genome Analysis Toolkit ; Blast algorithms for nucleotide- and protein-based sequence searching; BWA-ALN , software for mapping low-divergent sequences to a reference genome; and MPI-HMMER , protein sequence analysis software. The company has also released optimized code for AMBER and NAMD, both of which are used for simulating the molecular dynamics of biomolecular systems. The Intel website provides performance numbers for each of the optimized codes as well as directions for h...

The National Center for Biotechnology Information  is asking for the bioinformatics community's input on a  proposed Blast XML specification update planned for release in the summer of 2014. The update, according to the development team, is intended to improve the consistency of the Blast output with XML standards as well as put in place new and useful elements. Blast XML users can submit their feedback at  this link .

Microbial Genomes Curator @ Computercraft Corporation--Maryland (US).  Submitted by Computercraft Corporation; posted on Saturday, March 17, 2012 RESPONSIBILITIES: Computercraft seeks a microbiologist to work with a team of software developers and biologists on microbial genome analysis including pan-genome, protein clusters, phylogenetic tree and more. This is a technically challenging position requiring experience in genome sequencing and annotation. A background in comparative genome analysis such as alignments and tree building is a plus. Our scientists work with genomic experts at the NIH's National Center for Biotechnology Information (NCBI) to create and enhance a suite of databases and tools available to researchers worldwide. Teamwork interaction and excellent organizational skills are essential for this detail-oriented position, as is scientific problem-solving with a results-oriented focus. REQUIREMENTS: * PhD in molecular biology, microbiology, or related field * ...

BIBI automates DNA sequence analysis for bacterial identification in the clinical field. BIBI relies on the use of BLAST and CLUSTAL W programs applied to different subsets of sequences extracted from GenBank. These sequences are filtered and stored in a new database, which is adapted to bacterial identification. For further details refer : http://umr5558-sud-str1.univ-lyon1.fr/ lebibi/lebibi.cgi

It is more user friendly and easy to use for those new to Linux. Contains all the necessary Bioinformatics tools. BioPuppy contains extensive help files for ALL its programs and Bioinformatcis tools with screen shot.   Sequence Analysis tools such as: Genewise, Muscle, Sigma etc are already embedded.   Structure Prediction tools such as: Phylogibbs, Mfold, FastLink are present.   Protein Structure Analysis Tools like Rasmol and Phylogenetic Analysis Tools such as FastDNA and Philip are already embedded. Most Importantly Molecular Dynamics tools such as GROMACS, Statistical Analysis Tools such as R and BioConductor are pre-loaded. It also contains BLAST, EMBOSS, Biofox and other online tools also. Install BioPuppy and experience all these features.   Welcome to  BioPuppy  Linux  

In structural biology, similarity analysis of protein structure is a crucial step in studying the relationship between proteins. Despite the considerable number of techniques that have been explored within the past two decades, the development of new alternative methods is still an active research area due to the need for high performance tools. Results: In this paper, we present TS-AMIR, a Topology String Alignment Method for Intensive Rapid comparison of protein structures. The proposed method works in two stages: In the first stage, the method generates a topology string based on the geometric details of secondary structure elements, and then, utilizes an n-gram modelling technique over entropy concept to capture similarities in these strings. This initial correspondence map between secondary structure elements is submitted to the second stage in order to obtain the alignment at the residue level. Applying the Kabsch method, a heuristic step-by-step algorithm is adopted in the secon...

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/9/82 Abstract Background The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Results Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages d...