<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/30976?offset=680 https://bioinformaticsonline.com/file/view/4482/bioinformatics-definitions-and-applications Thu, 12 Sep 2013 15:04:36 -0500 https://bioinformaticsonline.com/file/view/4482/bioinformatics-definitions-and-applications <![CDATA[Bioinformatics definitions and applications !!!]]> There have been long discussion amongst several specialized/expert educator regarding bioinformatics arena, but everyone explain bioinformatics with their own view. I tried to explain it with a cartoon. Hope you all will like it.

]]> Jit https://bioinformaticsonline.com/news/view/44515/cleaner-blast-databases-for-more-accurate-results Tue, 23 Apr 2024 01:23:08 -0500 https://bioinformaticsonline.com/news/view/44515/cleaner-blast-databases-for-more-accurate-results <![CDATA[Cleaner BLAST Databases for More Accurate Results]]> 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. 

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

]]> LEGE https://bioinformaticsonline.com/opportunity/view/4575/hiv-phd-and-msc-research-positions Mon, 16 Sep 2013 18:55:44 -0500 <![CDATA[HIV PhD and MSc Research Positions]]> SANBI are looking to recruit two MSc students and a PhD student who are interested in implementing a computational biology approach to explore HIV’s glycan shield. Successful candidates for the MSc should hold an honours degree in physics, computer science or biological sciences while PhD applicants should hold an honours degree and a MSc in one or more of physics, computer science or biological sciences.

As these positions are funded by the South African National Research Foundation (NRF) priority will be given to South African citizens and permanent residents however exceptional applicants who do not fulfil these criteria may be considered.

Applications including a CV outlining your experience together with a cover letter detailing why you are a suitable candidate should be sent to simon_at_sanbi.ac.za by 30th September 2013.

More @ http://www.sanbi.ac.za/hiv-phd-and-msc-research-positions/

]]> https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6 Wed, 27 Jun 2018 18:38:21 -0500 https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6 <![CDATA[Understanding BLASTn output format 6 !]]> 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"

]]> Rahul Nayak https://bioinformaticsonline.com/researchlabs/view/4657/giovanni-parmigiani-lab Fri, 20 Sep 2013 13:21:41 -0500 <![CDATA[Giovanni Parmigiani Lab]]> Scientific Interests:

Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.

Statistical methods for the analysis of high throughput genomic data: analysis of cancer genome sequencing projects; integration of genomic information across technologies; cross-study validation of genomics results.

Statistical methods for comparative effectiveness research: comprehensive models for lifetime history of chronic disease outcomes; Bayesian meta-analysis; Bayesian causal inference; decision analysis.

Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design and their application to adaptive and multistage studies in clinical and epidemiological research.

http://bcb.dfci.harvard.edu/~gp/index.html

http://scholar.google.com/citations?user=OlpYP3UAAAAJ&hl=en

]]> https://bioinformaticsonline.com/blog/view/43424/rest-api Mon, 04 Oct 2021 12:46:40 -0500 https://bioinformaticsonline.com/blog/view/43424/rest-api <![CDATA[REST API]]> 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.

]]> Neel https://bioinformaticsonline.com/researchlabs/view/4755/sundar-lab Mon, 23 Sep 2013 11:10:16 -0500 <![CDATA[Sundar Lab]]> Area of interest

Understanding DNA-protein interactions, genome engineering
Computational Genomics and Bioinformatics
Secondary metabolite biosynthesis, metabolic engineering

Ongoing Projects:

"Betraying the parasite’s redox system: Studies on spermidine synthase of Leishmania donovani "

"Towards modifying nature's DNA-recognition system"

"Yield enhancement strategies for production of therapeutic compounds by cell and tissue cultures of Tinospora cordifolia (willd.) Miers ex Hook. F. & Thoms"

"Program support for Computational Genomics"

More at http://web.iitd.ac.in/~sundar/

]]> https://bioinformaticsonline.com/bookmarks/view/38449/koala-keggs-internal-annotation-tool-for-k-number-assignment-of-kegg-genes-using-ssearch-computation Wed, 12 Dec 2018 09:16:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38449/koala-keggs-internal-annotation-tool-for-k-number-assignment-of-kegg-genes-using-ssearch-computation <![CDATA[KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation]]> KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode.    See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

]]> Abhimanyu Singh https://bioinformaticsonline.com/researchlabs/view/5210/sandelin-group Mon, 30 Sep 2013 19:12:58 -0500 <![CDATA[Sandelin group]]> Sandelin group have a deep interest in most biology, but focus on gene regulation and the many areas that are connected with this, including transcriptomics, epigenetics and technological and informatics aspects.

The group is both computational and experimental.

We ask biological questions to large datasets made using novel genomics techniques, with the help of computers. One of the strengths in the group are the many connections to high-profile experimental laboratories which supply data to be analyzed.

Lab webpage @ http://people.binf.ku.dk/albin/Sandelin_group_at_the_Bioinformatic_Centre/The_Sandelin_group.html

]]> https://bioinformaticsonline.com/news/view/4590/tigers-genome-sequenced Tue, 17 Sep 2013 16:48:24 -0500 https://bioinformaticsonline.com/news/view/4590/tigers-genome-sequenced <![CDATA[Tigers genome sequenced]]> Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger. 

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

]]> Rahul Agarwal