BOL: Related items

The anatomy of successful computational biology software

Jitendra Narayan — Thu, 10 Oct 2013 11:53:08 -0500

Creators of software widely used in computational biology discuss the factors that contributed to their success

Nature Biotechnology spoke with Altschul and several other originators of computational biology software programs widely used today (Table 1). The conversations explored what makes certain software tools successful, the unique challenges of developing them for biological research and how the field of computational biology, as a whole, can move research agendas forward. What follows is an edited compilation of interviews.

Detail @ http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html

News Source @ Nature

Cleaner BLAST Databases for More Accurate Results

LEGE — Tue, 23 Apr 2024 01:23:08 -0500

Do you use BLAST to identify a sequence or the evolutionary scope of a gene? That can be challenging if contaminated and misclassified sequences are in the BLAST databases and show up in your search results. To address this problem, we now use the NCBI quality assurance tools listed below to systematically remove these misleading sequences from the default nucleotide (nt) and protein (nr) BLAST databases.

Foreign Contamination Screen tool for genome cross-species screening (FCS-GX) detects contamination from foreign organisms in genomes and other sequences using the genome cross-species aligner (GX)
Average Nucleotide Identity (ANI) evaluates the taxonomic classification of prokaryotic genome assemblies. Sequences from genomes marked up as ‘unverified source organism’ are considered suspect and removed.

Ref https://ncbiinsights.ncbi.nlm.nih.gov/2024/04/22/cleaner-blast-databases-more-accurate-results/

Network Analysis @ Indian Statistical Institute

Wed, 16 Oct 2013 08:06:50 -0500

Indian Statistical Institute Kolkata invites applications for the following posts

2013 Oct Advertisement from Indian Statistical Institute

Post: Network Analysis

No. of Positions: 01

Educational Qualifications:

Candidate should have passed BE/B.Tech Or Equivalent in Computer Science / Electrical Engineering / Electronics / Information Technology / Bioinformatics / Biotechnology with throughout first Class
Experience:

(details of experience required)
Pay Scale: INR Rs.16000-20000/-P.M.

Walk-In-Interview : 22 Oct 2013 at 10:30 AM

Download Official Notification:
http://www.isical.ac.in/JobApplicationFiles/MIU_0310201311433700.pdf

Understanding BLASTn output format 6 !

Rahul Nayak — Wed, 27 Jun 2018 18:38:21 -0500

BLASTn output format 6

BLASTn maps DNA against DNA, for example gene sequences against a reference genome

blastn -query genes.ffn -subject genome.fna -outfmt 6

BLASTn tabular output format 6

Column headers:
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

1.	qseqid	query (e.g., gene) sequence id
2.	sseqid	subject (e.g., reference genome) sequence id
3.	pident	percentage of identical matches
4.	length	alignment length
5.	mismatch	number of mismatches
6.	gapopen	number of gap openings
7.	qstart	start of alignment in query
8.	qend	end of alignment in query
9.	sstart	start of alignment in subject
10.	send	end of alignment in subject
11.	evalue	expect value
12.	bitscore	bit score

Define your own output format

by adding the option -outfmt, as for example:

-outfmt "6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore"

supported format specifiers are:
qseqid    Query Seq-id
qgi   Query GI
qacc    Query accesion
qaccver   Query accesion.version
qlen    Query sequence length
sseqid    Subject Seq-id
sallseqid All subject Seq-id(s), separated by a ';'
sgi       Subject GI
sallgi    All subject GIs
sacc      Subject accession
saccver   Subject accession.version
sallacc   All subject accessions
slen      Subject sequence length
qstart    Start of alignment in query
qend    End of alignment in query
sstart    Start of alignment in subject
send      End of alignment in subject
qseq      Aligned part of query sequence
sseq      Aligned part of subject sequence
evalue    Expect value
bitscore  Bit score
score   Raw score
length    Alignment length
pident    Percentage of identical matches
nident    Number of identical matches
mismatch  Number of mismatches
positive  Number of positive-scoring matches
gapopen   Number of gap openings
gaps      Total number of gaps
ppos      Percentage of positive-scoring matches
frames    Query and subject frames separated by a '/'
qframe    Query frame
sframe    Subject frame
btop      Blast traceback operations (BTOP)
staxids   Subject Taxonomy ID(s), separated by a ';'
sscinames Subject Scientific Name(s), separated by a ';'
scomnames Subject Common Name(s), separated by a ';'
sblastnames Subject Blast Name(s), separated by a ';'   (in alphabetical order)
sskingdoms  Subject Super Kingdom(s), separated by a ';'     (in alphabetical order)
stitle    Subject Title
salltitles  All Subject Title(s), separated by a '<>'
sstrand   Subject Strand
qcovs   Query Coverage Per Subject
qcovhsp   Query Coverage Per HSP

default values are:
-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"

Troyanskaya Lab

Fri, 18 Oct 2013 10:57:40 -0500

In our research, we combine computational methods with an experimental component in a unified effort to develop comprehensive descriptions of genetic systems of cellular controls, including those whose malfunctioning becomes the basis of genetic disorders, such as cancer, and others whose failure might produce developmental defects in model systems.

Research Interest
Genomic Data Integration

Microarray Analysis

Gene and Protein Function Prediction

Detection and Analysis of Chromosomal Abnormalities and Functional Evolution

Integration of Computation and Experiments

Identification of Biological Networks and Pathways

Evaluation and Validation of Computational Predictions

Scalable Visualization-Based Data Analysis

More @ http://reducio.princeton.edu/cm/
PI page @ http://reducio.princeton.edu/cm/ogt

REST API

Neel — Mon, 04 Oct 2021 12:46:40 -0500

REST API

The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language	Download	Requirements
Perl	psiblast.pl	LWP and XML::Simple
Python	psiblast.py	xmltramp2

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

Assistant Professor in Molecular Synthesis for Drug Discovery and Development @ CBMR, Lucknow

Wed, 30 Oct 2013 06:42:27 -0500

ADVERTISEMENT FOR FACULTY POSITIONS AT CENTRE OF BIOMEDICAL RESEARCH (CBMR), LUCKNOW

Details of the Positions and Pay Structure:

03 Posts for Assistant Professor in Molecular Synthesis for Drug Discovery and Development

Essential Qualifications and Requirements:

1. PhD in Synthetic Organic Chemistry/Medicinal Chemistry with research publications in high quality international journals and first class grade at the preceding degree from recognised University/Institute in India or abroad with consistently good academic record.
2. Three Yrs of Post-doctoral experience in relevant area.
3. Below 35 Yrs of age at the time of application

Desirable Experience: Candidates having strong research background in organic synthesis, total synthesis of structurally complex and medicinally important natural products/drugs related to cancer, neurodegenerative diseases (neurotropically active molecules for Alzheimer's, Parkinson’s, dementia etc) and infectious diseases such as malaria, TB etc. will be preferred.

Interested candidates may apply with:

1. Filled up Application Form (download from CBMR Website: http://www.cbmr.res.in) along with the Cover Letter, Curriculum Vitae including academic record (Bachelor degree onwards), awards, honours, list of Publications and reprints of 5 best publications.
2. Proposed research plan (max 3-4 pages).
3. Names and address (with valid e-mail and Phone number) of at least 3 academic referees.
4. Online Payment Receipt with transaction reference no. of Rs. 1000/- (USD 100 or equivalent foreign currency) on following details.
Account Number: 30054847814 Name: Director, Centre of Biomedical Research
Bank: STATE BANK OF INDIA, SGPGI Campus Branch, LUCKNOW

IFSC Code: SBIN0007789
MICR No: 22602034

Applications can be sent by registered/speed post or by e-mail to the following address:

The Director,
Centre of Biomedical Research (CBMR),
Sanjay Gandhi PGI Campus,
Raebareli Road, Lucknow-226014
e-mail: cbmr.admin@cbmr.res.in,
gp.pandey@cbmr.res.in

More Info:

http://www.cbmr.res.in/career/Advertisement%20for%20the%20post%20of%20Professors%20and%20Assistant%20Professors.pdf

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

Junior Bioinformatic position

Wed, 26 Aug 2015 05:35:28 -0500

Junior Bioinformatic position in the laboratory of Inflammation and immunology in cardiovascular pathologies at Humanitas:

We are seeking a highly motivated young PhD student with strong interest in high throughput data analysis.
Detailed descriptions of our recent research activities may be found here:
http://www.humanitas-research.org/condorelli-gianluigi-md-phd/

Position is available starting from October/November. A probationary period of one month will be required.

Please send a CV along with a cover letter stating the reasons for applying and contact details of one or more referees to Dr. Paolo Kunderfranco (paolo.kunderfranco@humanitasresearch.it).

New born babies get ready to know their whole genome soon!!!

Rahul Agarwal — Thu, 05 Sep 2013 07:24:02 -0500

USA launch a pilot projects to examine medical information of newborn baby, which are being funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health.

Awards of $5 million to four grantees have been made in fiscal year 2013 under the Genomic Sequencing and Newborn Screening Disorders research program. The program will be funded at $25 million over five years, as funds are made available.

"Hundreds of US babies will be pioneers in genomic medicine through a US$25-million programme to sequence their genomes soon after they are born."

Source:

http://blogs.nature.com/news/2013/09/scientists-to-sequence-hundreds-of-newborns-genomes.html

http://www.genome.gov/27554919

BOL: Related items

The anatomy of successful computational biology software

Cleaner BLAST Databases for More Accurate Results

Network Analysis @ Indian Statistical Institute

Understanding BLASTn output format 6 !

BLASTn output format 6

BLASTn tabular output format 6

Define your own output format

Troyanskaya Lab

REST API

REST API

Python

Assistant Professor in Molecular Synthesis for Drug Discovery and Development @ CBMR, Lucknow

BEAP: Blast Extension and Assembly Program

Junior Bioinformatic position

New born babies get ready to know their whole genome soon!!!