BOL: Related items

Basics of BLAST Programs !

BioStar — Fri, 26 Jul 2024 06:04:26 -0500

The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy

Tue, 11 Feb 2014 08:06:47 -0600

We are seeking one motivated scientist to analyze genomics and transcriptomics data of a large collection of neuroblastoma tumors. The successful candidate will be part of a team of researchers with extensive expertise in genome cancer study. He/she will be involved in the analysis of DNA-seq, RNA-seq, ChIP-seq data using available methods running in R and UNIX environment.

Qualifications

PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.

Application

Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.

Contacts

Start date: 1° April 2014
Salary on grant: 25,000 euros per year.
Contact Person (Referent): Mario Capasso
Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it
Tel: +39 081 3737889

GenXPro GmbH

Rahul Agarwal — Thu, 22 May 2014 07:18:35 -0500

GenXPro GMbH is service provider for entire spectrum of nucleotide-based information of any biological sample. By combining intelligent data reduction techniques and latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solutions for transcriptomic-, genomic- or epigenomic research.

GENXPRO GMBH, ALTENHÖFERALLEE 3, 60438 FRANKFURT MAIN, GERMANY

Website: http://www.genxpro.info/products_and_services/

PHONE: +49 (0)69- 95 73 97 10, FAX: +49 (0)69- 95 73 97 06

EMAIL: info@genxpro.de

NGSymposium in Computational Biology

Mon, 09 Mar 2020 06:00:30 -0500

We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.

Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!

Registration of passive participants will be open after closing of registration of active participants.

Details an registration: https://ngschool.eu/conference/

World promising health companies !

Rahul Nayak — Tue, 31 Dec 2019 19:10:13 -0600

The health care industry is expected to sustain stable growth over the next decade for a variety of reasons. Advances in medicine have prolonged the average lifespans of most people, requiring more health care treatments over longer terms. In years past, once people turned 65 and enrolled in Medicare, they were expected to live another 10 to 20 years.

Biohub is a joint collaborative effort by Berkeley, UCSF and Stanford for a medical science research center funded by a $600 million commitment from Facebook CEO and founder Mark Zuckerberg and his wife Priscilla Chan. It is trademarked as well as CZ Biohub. It is currently co-led by Stephen Quake and Joseph DeRisi.

More at https://www.czbiohub.org/

Calico LLC is an American research and development biotech company founded on September 18, 2013 by Bill Maris and backed by Google with the goal of combating aging and associated diseases. In Google's 2013 Founders' Letter, Larry Page described Calico as a company focused on "health, well-being, and longevity".

More at https://www.calicolabs.com/

UnitedHealth Group, Inc. (UNH) is the largest health care services company in the world, serving over 50 million individuals in the United States as of late 2018 and 5 million in Brazil. The company provides a wide range of health care products and services, such as health maintenance organizations (HMOs), point of service plans (POS), preferred provider organizations (PPOs), and managed fee-for-service programs.

More at https://www.unitedhealthgroup.com/

Sequanix: a dynamic graphical interface for Snakemake workflows

BioStar — Wed, 12 Feb 2020 01:20:34 -0600

A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).
A set of pipelines dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework) with more than 80 re-usable rules (see Rules).
Original tools to help in the creation of such pipelines including HTML reports.
Standalone applications:
1. sequana_coverage ease the extraction of genomic regions of interest and genome coverage information
2. sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.
3. Sequanix: GUI for snakemake workflows, a GUI for Snakemake workflows (hence Sequana pipelines as well)
More at https://sequana.readthedocs.io/en/master/

Address of the bookmark: https://github.com/sequana/sequana

Rolf Backofen Lab

Thu, 18 Jul 2013 13:51:23 -0500

The research interest of this group include constraint programming, structure prediction in simplified protein models, investigation of protein energy landscapes, detection of RNA sequence/structure motifs, prediction and evaluation of alternative splice forms, description and detection of regulatory sequences.

Link @ http://www.bioinf.uni-freiburg.de/

Vvek's Lab

Thu, 26 Sep 2013 11:11:39 -0500

Broad Area of Research: RNA biology (microRNA, lncRNA), Stem cells, Functional genomics, Epigenomics and Cancer

RNAs, especially non-coding RNAs (such as microRNA, long ncRNAs) are recently identified to be very abundant in mammalian organisms and play some key roles in gene expression regulation, gene silencing, and also implicated in disease progression, stem cell pluripotency etc. Current research activities of our lab include analysis of expression pattern of ncRNAs by microarray and next-gen sequencing data and understanding the role of miRNAs or other regulatory RNAs in various diseases, especially cancer and validation by reporter assays (renilla/luciferase) and other experimental tools.

More @ http://vvekslab.in/index.html

Roderic Guigó Lab

Mon, 01 Sep 2014 17:13:00 -0500

Research in our group focuses on the investigation of the signals involved in gene specification in genomic sequences (promoter elements, splice sites, translation initiation sites, etc…). We are interested both in the mechanism of their recognition and processing, and in their evolution. In addition, but related to this basic component of our research, our group is also involved in the development of software for gene prediction and annotation in genomic sequences. Our group also actively participates in the analysis of many eukaryotic genomes and it in involved in the NIH-funded ENCODE project. Furthermore we are members of two large cancer-studies consortia (chronic lymphocytic leukemia "CLL" and Breast Cancer -Hospital del Mar/CRG/Roche-).

More at http://big.crg.cat/computational_biology_of_rna_processing

Chekulaevalab

Tue, 12 Jan 2016 02:32:03 -0600

Focusing on understanding the molecular mechanisms that regulate mRNA translation, localization and stability and role of non-coding RNAs in this process. Up to 90% of human DNA is estimated to be transcribed into so called non-coding RNAs that are not translated into proteins. Many of them act as potent modifiers of gene expression. miRNAs are a class of such short non-coding RNAs. They regulate expression of more than a half of eukaryotic genes, thus, affecting multiple biological processes, including cell proliferation, differentiation, apoptosis and senescence. Not surprisingly, miRNAs are involved in many human pathologies, including cancer and neurological disorders and hold great potential as drug targets, disease markers, as well as therapeutic agents.
Our lab is located at the Berlin Institute for Medical Systems Biology (BIMSB), a part of the Max Delbrück Center for Molecular Medicine (MDC).

http://www.chekulaevalab.org/