BOL: Related items

Bioinformatics Training Material !

BioStar — Sat, 18 Mar 2023 11:26:18 -0500

Glittr is a curated list of bioinformatics training material.
All material is:

In a GitHub or GitLab repository
Free to use
Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Research Associate (RA) at INSTITUTE OF ADVANCED STUDY IN SCIENCE AND TECHNOLOGY

Mon, 05 May 2014 08:44:24 -0500

INSTITUTE OF ADVANCED STUDY IN SCIENCE AND TECHNOLOGY
(An Autonomous Institute under Department of Science and Technology, Govt. of India)
Paschim Boragaon, Garchuk, Guwahati-781035

Appointment Adv.No.2

Applications in plain paper are invited from Indian citizens for one/two position each of Research Associate, Traineeship and Studentship for BIF facility, Division of Life Sciences, IASST.

Applications with complete Bio-data containing contact address, e-mail and phone number, two recent passport size photographs and attested copies of mark sheets, certificates etc., should be sent to the Registrar, IASST, Paschim Boragaon, Garchuk, Guwahati – 781035, Assam, so as to reach on or before 5/05/2014.

A. Research Associate:

Number of vacancies: 1 (One)

Qualifications:

PhD in Bioinformatics or allied disciplines with knowledge of Bioinformatics. The candidates who have submitted PhD thesis may also apply.

In case, candidates having PhD are not found, candidates having MSc in Bioinformatics or allied disciplines with sound knowledge of Bioinformatics will be preferred.

Remuneration: Candidate having PhD will get a consolidated remuneration of Rs. 22,000/- +HRA per month. MSc having NET/GATE/SLET qualified candidate will get a remuneration of Rs. 16,000/= and HRA and candidate with only MSc will get a remuneration of Rs.14,000/- and HRA.

Tenure:

The post is initially for one year and may be extended depending on the performance till the tenure of the project.

B. Traineeship:

Number of vacancies: 2 (Two)

Qualifications:

Candidate with a postgraduate degree in Bioinformatics/Biotechnology/Life sciences from a recognised University

Remuneration: Rs. 5000/month for 6 months

C. Studentship:

Number of vacancies: 2 (Two)

Qualifications:

Candidate pursuing M.Sc in bioinformatics in a recognised University.

Remuneration: Rs. 5000/month for 6 months

http://iasst.gov.in/pdf/recruitment/advt%20no_2_24042014.pdf

16sRNA Database Download

LEGE — Wed, 24 Apr 2024 04:33:15 -0500

Downloading 16S rRNA databases can be crucial for various bioinformatics analyses, especially in microbiome research. However, it's important to note that databases can vary based on your specific needs, such as the taxonomic coverage you require or the type of analysis you're performing. Here's a general guideline on how you can obtain 16S rRNA databases:

NCBI (National Center for Biotechnology Information):
- NCBI provides various databases related to genetic information, including 16S rRNA sequences.
- You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
- Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
- You can download sequences individually or in batches using the provided tools.
GreenGenes:
- GreenGenes is a widely used 16S rRNA gene sequence database.
- You can access it at http://greengenes.secondgenome.com/.
- GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.
SILVA:
- SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
- It covers not only 16S rRNA but also other ribosomal RNA sequences.
- SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.
Ribosomal Database Project (RDP):
- RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
- It provides tools for sequence analysis and classification.
- You can download sequences and taxonomy information from their website.
QIIME (Quantitative Insights Into Microbial Ecology):
- QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
- It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
- QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

“On” and “Off” the neuron !!!

Rahul Nayak — Fri, 25 Apr 2014 19:31:13 -0500

Optogenetics is a recent innovation in neuroscience that gives researchers the ability to control the activity of neurons with light. With this powerful tool, researchers are teasing apart the biological basis of memory, behavior, and disease (see “Scientists Make Mice ‘Remember’ Things That Didn’t Happen” and “An On-Off Switch for Anxiety,”). But for the first several years of this technology’s existence, the proteins that scientists added to neurons to make them react to light were only good at activating neurons. That limited researchers’ ability to understand neuronal circuits, sets of interconnected neurons that are thought to control behavior and, when misfiring, to underlie many brain conditions. Problems can arise from any imbalance in circuit activity, whether too much or too little.

Now, two research groups have engineered new optogenetic proteins that can be used to efficiently silence neurons. One of the two new proteins comes from the lab of Karl Deisseroth, a psychiatrist and neuroscientist at Stanford University who helped develop optogenetics as a research tool. His group’s new “off” switch for neurons was created by changing 10 of the 333 amino acids in an existing optogenetic protein, which itself had been engineered by combining natural proteins from green algae. That advance “creates a powerful tool that allows neuroscientists to apply a brake in any specific circuit with millisecond precision,” said Thomas Insel, director of the National Institute of Mental Health, in a released statement. The other new silencing protein, developed by scientists at the Humboldt University of Berlin and collaborators, was created by changing amino acids in the same existing optogenetic protein.

Some researchers are also looking to optogenetics as a potential treatment for patients with a variety of conditions (see “For Mice, and Maybe Men, Pain Is Gone in a Flash,” and “Flipping on the Lights to Halt Seizures”) but there are huge challenges to overcome. The method requires genetic modification of cells to make them light-sensitive. It also requires implanted light sources for all but the shallowest of nerve endings.

ICGEB Bioinformatics Vacancy !

Mon, 09 Nov 2020 07:34:49 -0600

The following vacancy is available in the DBT Apex Biotechnology Information Center (BTIC) Project at ICGEB, New Delhi, India.

Name of the Post: Senior Information Scientist

No. of Posts: 01

Tenure of Job: The position is available for a period of 6 months, which will be extended
based on the performance of work.

How to Apply for ICGEB Vacancy:

Interested candidates must submit their full, updated Curriculum Vitae with a detailed description of pertinent experience, together with two references by 19th November 2020 addressed to The Chairperson, DBT- Apex BTIC, ICGEB, Aruna Asaf Ali Marg, New Delhi 110067, Email: abtic@icgeb.res.in, kindly write “Application for SIS, DBT Apex BTIC” in the subject of the e-mail or envelope, if sending by post.

Shortlisted applicants will be invited for an interview at ICGEB. Just the selected applicants will certainly be informed individually. No TA/DA or accommodation will be offered to the candidates attending the interview.

More at https://www.icgeb.org/positions-for-a-senior-information-scientist-dbt-apex-btic/

Elastic BLAST !

Abhi — Tue, 06 Sep 2022 18:14:57 -0500

ElasticBLAST is a new way to BLAST large numbers of queries, faster and on the cloud. Here are the top three reasons you should use ElasticBLAST:

1. ElasticBLAST can handle much LARGER queries!

ElasticBLAST can search query sets that have hundreds to millions of sequences and against BLAST databases of all sizes.

2. ElasticBLAST is FASTER

ElasticBLAST distributes your searches across multiple cloud instances to process them simultaneously. The ability to scale resources in this way allows you to process large numbers of queries in a shorter time than you could with BLAST+.

3. ElasticBLAST is EASY to run on the cloud

ElasticBLAST is easy to set up using our step-by-step instructions (Amazon Web Services (AWS), Google Cloud Platform (GCP)) and allows you to leverage the power of the cloud. Once configured, it manages the software and database installation, handles partitioning of the BLAST workload among the various instances, and deallocates cloud resources when the searches are done.

ElasticBLAST also selects the instance (i.e., machine) type for you based on database size. Of course, you can also choose the instance type manually if you prefer.

Address of the bookmark: https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/

Assistant Professor at Jawaharlal Nehru University in Delhi

Wed, 07 May 2014 00:29:22 -0500

Advt. No. RC/48/2014

SCHOOL OF COMPUTATIONAL AND INTEGRATIVE SCIENCES (SC&IS)

ESSENTIAL QUALIFICATION : - M.Sc./M.Tech. in Physics/ Chemistry/ Biology/ Mathematics/ Statistics/ Bioinformatics/ Computational Biology. Ph.D. in the broad areas of Bioinformatics/ Computational Biology. Candidates must have demonstrated capabilities in terms of high impact research publications in either of the above mentioned areas.

Scale of Pay : - 15600-39100/- (PB-III) AGP Rs. 6000/-

For more details on Centre/School, Specializations etc. please visit JNU website www.jnu.ac.in or contact Section Officer, Room Nos. 131-132, Recruitment Cell, Administrative Block, JNU, New Delhi – 110067, Email: recruitmentjnu2013@gmail.com The last date for the receipt of application is 15 May, 2014.

http://www.jnu.ac.in/Career/

http://www.jnu.ac.in/Career/ADVTNo_RC_48_2014.pdf
Last Apply Date:

15 May 2014

Basic command-line to run BLAST

Shruti Paniwala — Wed, 14 Mar 2018 05:10:34 -0500

The goal of this tutorial is to run you through a demonstration of the command line, which you may not have seen or used much before.

All of the commands below can copy/pasted.

Install software

Copy and paste the following commands

sudo apt-get update && sudo apt-get -y install python ncbi-blast+

This updates the software list and installs the Python programming language and NCBI BLAST+.

Get Data

Grab some data to play with. Grab some cow and human RefSeq proteins:

wget ftp://ftp.ncbi.nih.gov/refseq/B_taurus/mRNA_Prot/cow.1.protein.faa.gz
wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.1.protein.faa.gz

This is only the first part of the human and cow protein files - there are 24 files total for human.

The database files are both gzipped, so lets unzip them

gunzip *gz
ls

Take a look at the head of each file:

head cow.1.protein.faa
head human.1.protein.faa

These are protein sequences in FASTA format. FASTA format is something many of you have probably seen in one form or another – it’s pretty ubiquitous. It’s just a text file, containing records; each record starts with a line beginning with a ‘>’, and then contains one or more lines of sequence text.

Note that the files are in fasta format, even though they end if ”.faa” instead of the usual ”.fasta”. This NCBI’s way of denoting that this is a fasta file with amino acids instead of nucleotides.

How many sequences are in each one?

grep -c '^>' cow.1.protein.faa
grep -c '^>' human.1.protein.faa

This grep command uses the c flag, which reports a count of lines with match to the pattern. In this case, the pattern is a regular expression, meaning match only lines that begin with a >.

This is a bit too big, lets take a smaller set for practice. Lets take the first two sequences of the cow proteins, which we can see are on the first 6 lines

head -6 cow.1.protein.faa > cow.small.faa

BLAST

Now we can blast these two cow sequences against the set of human sequences. First, we need to tell blast about our database. BLAST needs to do some pre-work on the database file prior to searching. This helps to make the software work a lot faster. Because you installed your own version of the sotware, you need to tell the shell where the software is located. Use the full path and the makeblastdb command:

makeblastdb -in human.1.protein.faa -dbtype prot
ls

Note that this makes a lot of extra files, with the same name as the database plus new extensions (.pin, .psq, etc). To make blast work, these files, called index files, must be in the same directory as the fasta file.

blastp [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-seg SEG_options] [-soft_masking soft_masking]
[-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]
[-best_hit_overhang float_value] [-best_hit_score_edge float_value]
[-window_size int_value] [-lcase_masking] [-query_loc range]
[-parse_deflines] [-outfmt format] [-show_gis]
[-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-ungapped] [-remote] [-comp_based_stats compo]
[-use_sw_tback] [-version]

Now we can run the blast job. We will use blastp, which is appropriate for protein to protein comparisons.

blastp -query cow.small.faa -db human.1.protein.faa

This gives us a lot of information on the terminal screen. But this is difficult to save and use later - Blast also gives the option of saving the text to a file.

    blastp -query cow.small.faa -db human.1.protein.faa -out cow_vs_human_blast_results.txt
ls

Take a look at the results using less. Note that there can be more than one match between the query and the same subject. These are referred to as high-scoring segment pairs (HSPs).

less cow_vs_human_blast_results.txt

So how do you know about all the options, such as the flag to create an output file? Lets also take a look at the help pages. Unfortunately there are no man pages (those are usually reserved for shell commands, but some software authors will provide them as well), but there is a text help output

blastp -help

To scroll through slowly

blastp -help | less

To quit the less screen, press the q key.

Parameters of interest include the -evalue (Default is 10?!?) and the -outfmt

Lets filter for more statistically significant matches with a different output format:

blastp \
-query cow.small.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 7

I broke the long single command into many lines with by “escaping” the newline. That forward slash tells the command line “Wait, I’m not done yet!”. So it waits for the next line of the command before executing.

Check out the results with less.

Lets try a medium sized data set next

head -199 cow.1.protein.faa > cow.medium.faa

What size is this db?

grep -c '^>' cow.medium.faa

Lets run the blast again, but this time lets return only the best hit for each query.

blastp \
-query cow.medium.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 6 \
-max_target_seqs 1

Summary

Review:

command line programs such as blast use flags to get information about how and what to do
blast options can be found by typing blastp -help
break a command up over many lines by using `` to “escape” the new line

Blastn

blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
[-db_hard_mask filtering_algorithm] [-subject subject_input_file]
[-subject_loc range] [-query input_file] [-out output_file]
[-evalue evalue] [-word_size int_value] [-gapopen open_penalty]
[-gapextend extend_penalty] [-perc_identity float_value]
[-qcov_hsp_perc float_value] [-max_hsps int_value]
[-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.7.0+

Memories Can Be Passed Down Through DNA

Sat, 10 May 2014 21:24:10 -0500

The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how this process works, and if it might apply to humans as well. Read More: Parental olfactory experience influences behavior and neural structure in subsequent generations http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3594.html "Using olfactory molecular specificity, we examined the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood." What Is Epigenetics? http://www.sciencemag.org/content/330/6004/611 "The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)-genetics." Epigenetics http://en.wikipedia.org/wiki/Epigenetics Watch More: How to Change Your Genes https://www.youtube.com/watch?v=B5DU9lgbsSE TestTube Wild Card http://testtube.com/dnews/dnews-231-how-too-many-screens-affect-our-brain?utm_source=YT&utm_medium=DNews&utm_campaign=DNWC Is Sexiness Hereditary? https://www.youtube.com/watch?v=z6STRCncvM8 ____________________ DNews is dedicated to satisfying your curiosity and to bringing you mind-bending stories & perspectives you won't find anywhere else! New videos twice daily. Watch More DNews on TestTube http://testtube.com/dnews Subscribe now! http://www.youtube.com/subscription_center?add_user=dnewschannel DNews on Twitter http://twitter.com/dnews Anthony Carboni on Twitter http://twitter.com/acarboni Laci Green on Twitter http://twitter.com/gogreen18 Trace Dominguez on Twitter http://twitter.com/trace501 DNews on Facebook http://facebook.com/dnews DNews on Google+ http://gplus.to/dnews Discovery News http://discoverynews.com

Apache server setting !

Abhi — Fri, 29 Oct 2021 04:29:51 -0500

Apache is an open source web server that’s available for Linux servers free of charge.

In this tutorial we’ll be going through the steps of setting up an Apache server.

What you’ll learn

How to set up Apache
Some basic Apache configuration

Address of the bookmark: https://ubuntu.com/tutorials/install-and-configure-apache#3-creating-your-own-website