BOL: Related items

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

New Layout for BLAST ftp Database Site

Jit — Tue, 21 Jan 2020 11:57:11 -0600

As announced previously, the new default database version for BLAST+ is dbV5. To complete this transition, the ftp database site will be updated to support this change. We expect this change to happen around February 4^th, please adjust your scripts or procedures accordingly.

Here is a list of what is changing:

All databases at the root level will be dbV5.
The dbV5 file naming, “_v5” will be removed. Databases with no “_vX” descriptor will be dbV5.
dbV4 tarballs will be renamed with "_v4", files included in tarball will not be renamed.
dbV4 databases will be moved to a v4 subdirectory.
As of 1/13/20 the Cloud directory will be frozen with no more new entries.
The will be no more updates to dbV4 databases.
The FASTA directory will contain nr, nt, swissprot, and pdbaa files.

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.gov

Scientists map 17,294 proteins produced in human body

Jit — Thu, 29 May 2014 01:57:55 -0500

Indian scientists missed the genomic profiling bus, but they've more than made up for it by creating the first human proteome map which is an extension of the genomic study. Till now, here is no direct equivalent for the human proteome. But recently two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

New BLAST Core Nucleotide Database (core_nt)

LEGE — Tue, 13 Aug 2024 07:12:53 -0500

The Core Nucleotide Database (core_nt) is now the default nucleotide BLAST database. Core_nt is also available on the command line. You get faster searches & more focused results.

Core_nt contains the same eukaryotic transcript and gene-related sequences as nt. The core_nt database is nt without most eukaryotic chromosome sequences. Most nucleotide BLAST searches with core_nt will be similar to the nt database. However, core_nt is better than nt for accomplishing your most common BLAST search goals, such as identifying gene-related sequences like transcript sequences and complete bacterial chromosomes. This is because, in recent years, nt has acquired more low-relevance, non-annotated, and non-gene content.

Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/18/new-blast-core-nucleotide-database/

Genomics and Personalized Medicine

Sun, 01 Jun 2014 23:38:42 -0500

(October 20, 2009) Michael Snyder, Professor of Genetics and Chair of the Department of Genetics at Stanford, discusses advances in gene sequencing, the impact of genomics on medicine, the potential for personalized medicine. and efforts at Stanford to further study these issues. Stanford Mini Med School is a series arranged and directed by Stanford's School of Medicine, and presented by the Stanford Continuing Studies program. Featuring more than thirty distinguished, faculty, scientists and physicians from Stanford's medical school, the series offers students a dynamic introduction to the world of human biology, health and disease, and the groundbreaking changes taking place in medical research and health care. Stanford University http://www.stanford.edu Stanford University School of Medicine http://med.stanford.edu Stanford Continuing Studies http://continuingstudies.stanford.edu Stanford University Channel on YouTube: http://www.youtube.com/stanford

BLAST options, setting and defaults

Jit — Mon, 10 Dec 2018 08:29:37 -0600

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST.

A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes

	BLASTN	BLASTP	BLASTX	TBLASTN	TBLASTX	PSIBLAST
Gap opening penalty: cost to open a gap [integer]	default = 5	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 5
Gap extension penalty: cost to extend a gap [integer]	default = 2	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 2
Nucleic match: reward for a match in the BLAST portion of run [integer]	default = 1	n/a	n/a	n/a	n/a	default = 1
Nucleic mismatch: penalty for a mismatch in the blast portion of run [integer]	default = -3	n/a	n/a	n/a	n/a	default = -3
Expectation value: (E) [real]	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0
Word size: the size of the initial word that must be matched between the database and the query sequence	default = 11	default = 3	default = 3	default = 3	default = 3	default = 11
Max scores: Number of one-line descriptions (V) [Integer]	default = 25	default = 25	default = 25	default = 25	default = 25	default = 25
Max alignments: number of alignments to show (B) [integer]	default = 15	default = 15	default = 15	default = 15	default = 15	default = 15
Query filter: filter applied to the query sequence	default = DUST	default = SEG	default = SEG	default = SEG	default = SEG	default = DUST
Query genetic code: genetic code to be used in BLASTX translation of the query	n/a	n/a	default = universal	default = universal	default = universal	n/a
Matrix: substitution matrix to be used for amino acid comparisons	no default	default = blosum62	default = blosum62	default = blosum62	default = blosum62	no default

Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX

Gaps Open	Gap Extension
10	1
10	2
11	1
8	2
9	2

Address of the bookmark: https://www.arabidopsis.org/Blast/BLASToptions.jsp

Adhoc Bioinformatics Faculty Position @ NIT

Tue, 03 Jun 2014 16:19:52 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, DEPARTMENT OF BIOTECHNOLOGY, WARANGAL – 506 021, Andhra Pradesh

No.NITW/BT/2014/adhoc

APPLICATIONS ARE INVITED FOR THE APPOINTMENT OF ADHOC FACULTY ON CONTRACT BASIS IN THE DEAPARTMENT OF BIOTECHNOLOGY

Period of Contract: Initially the appointment is for one semester i.e., from July 2014 up to December 2014 only.

Essential Qualifications:

i) B. Tech or equivalent in Biotechnology/ Industrial Biotechnology/ Biochemical Engineering / Chemical Engg. Or M. Sc in Microbiology/ Botany/ Zoology/ Biochemistry/Biotechnology and ii) M. Tech or equivalent in Biotechnology/Industrial Biotechnology/Bioinformatics

Integrated M. Tech in Biotechnology/Industrial Biotechnology/ Bioinformatics

Candidates must possess First class (60% aggregate marks or 6.5 CGPA) at B. Tech/ M. Sc and M. Tech.

Desirable: Ph. D Pay Package: All selected candidates shall be eligible for a consolidated pay of Rs.30, 000/- per month. Candidates with Ph. D shall be eligible for an additional amount of Rs.5, 000/- per month.

How to apply : Applications on plain paper with attested photocopies of certificate and bio data along with justification for eligibility should reach to the Head, Department of Biotechnology, National Institute of Technology, Warangal AP 506004 in the form of soft or hard copy on or before 21st June 2014 email : biotech_hod@nitw.ac.in

Intimation: No separate call letters will be sent to the candidates. All the eligible candidates will be notified in the institute web site on 23rd June 2014. All the eligible candidates are requested to report for the interview to the Head, Department of Biotechnology at 9:00 AM on 27th June 2014

Joining: Selected candidates will be informed and they are expected to join immediately.

http://www.nitw.ac.in/nitw/announcements/2014/Bio-Adhoc%20Advt.%20May-2014.pdf

NCBIBLAST+ 2.14.1 now available

Neel — Wed, 30 Aug 2023 02:36:13 -0500

#NCBIBLAST+ 2.14.1 now available with improved documentation, faster and more reliable database downloads, and some bug fixes.

Check out the changes they made.

They added the cleanup-blastdb-volumes.py script to remove unused BLAST database volumes. Read the documentation here.

They also switched the protocol from ftp to https to access BLAST databases for increased performance and reliability when downloading data from the NCBI with the update_blastdb.pl script.

And fixed a few bugs related to downloading data from the NCBI, and mt_mode crashing blastn and blastx.

Check out the release notes.

Download BLAST+ 2.14.1

Questions or comments? Please write the BLAST help desk.

More info and download: https://blast.ncbi.nlm.nih.gov/doc/blast-news/2023-BLAST-News.html

Search Shell Command History

Rahul Nayak — Thu, 12 Jun 2014 17:43:34 -0500

We use couple of hundreads of command in daily basis. Most of them are actually repeated several time. The question remain open how do I search old command history under bash shell and modify or reuse it?

Now a days almost all modern shell allows you to search command history if enabled by user. Use history command to display the history list with line numbers. Lines listed with with a * have been modified by user.

Shell history search command

Type history at a shell prompt:
$ history

It will display the list of all used commandline history with an serial number.

To search particular command, enter:
$ history | grep command-name
$ history | egrep -i 'scp|ssh|ftp'
Emacs Line-Edit Mode Command History Searching

To get previous command containing string, hit [CTRL]+[r] followed by search string:

(reverse-i-search):

To get previous command, hit [CTRL]+[p]. You can also use up arrow key.

CTRL-p

To get next command, hit [CTRL]+[n]. You can also use down arrow key.

CTRL-n

fc command

Apart from hostory command there are fc command to extract the command from history. The fc stands for either "find command" or "fix command.

For example list last 10 command, enter:
$ fc -l 10
To list commands 130 through 150, enter:
$ fc -l 130 150
To list all commands since the last command beginning with ssh, enter:
$ fc -l ssh
You can edit commands 1 through 5 using vi text editor, enter:
$ fc -e vi 1 5

Delete command history

The -c option causes the history list to be cleared by deleting all of the entries:
$ history -c