BOL: Related items

Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.

Jit — Tue, 18 Jun 2019 05:33:04 -0500

Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding sequences.

Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete.

See a recent presentation on Cogent being applied to the Cuttlefish Iso-Seq data.

Cogent preliminary draft paper (updated 2016Dec version), Supplementary

Please see wiki for details on usage.

Address of the bookmark: https://github.com/Magdoll/Cogent

Research Associate @ INDIAN INSTITUTE OF SPICES RESEARCH

Wed, 25 Dec 2013 12:34:43 -0600

INDIAN INSTITUTE OF SPICES RESEARCH
(Indian Council of Agricultural Research)
Marikunnu P.O., Kozhikode – 673 012, Kerala

WALK -IN- TEST CUM INTERVIEW

Walk- in- Test cum Interview (based on test) for the selection of Research Associate (Bioinformatics) & Bioinformatic Trainees under the scheme ‘Distributed Information Sub Centre- DISC’ will be held at this Institute as per details indicated below.

Research Associate

Date of Interview : 21 -01-2014 at 10.00 A.M

Qualifications : a) Essential: Doctorate degree in Bioinformatics or Biotechnology/Life Sciences/Biochemistry with expertise in Bioinformatics as evidenced by publications.

Three years research experience after MVSc/MPharm/ME/MTech with Bioinformatics Specialization.

b Desirable: Experience in handling NGS data Programming skills in Python/Bioperl

Emoluments : Rs:22000/- per month + HRA (higher pay upto Rs.24000/- can be paid depending on the qualifications and experience.

Upper age limit : 40 years for Men & 45 years for Women as on date of Interview (Upper Age limits are relaxable for SC, ST and OBC candidates as per Govt. of India norms (at present 5 years for SC/ST and 3 years for OBC)

Duration of Project : Till the closure of the project.

General Terms and conditions

1. The above positions are purely on temporary basis and is co-terminus with the closure of the project. There is no provision of re-employment after termination of project. The selected candidate will not have any right for claiming pay scale or absorption against any regular post being vacant on a later date at this Institute.
2 . No TA/DA will be paid for attending the Interview.
3. Canvassing in any form will lead to cancellation of candidate.
4. The decision of Director, IISR would be final and binding in all aspects.
5. Candidates will not be permitted to enter the Examination Hall after 10.00 A.M.
6. Candidates who secure the minimum marks prescribed by the Institute in written test only will be eligible for calling for the interview. The number of candidates to be called for the interview will be decided by the Director of the Institute.
7 Those who do not possess original Degree/PG certificate or Provisional certificate will not be allowed to attend the Test/Interview.

Note: All relevant certificates (in original) and bio data
No objection certificate in case he/she is employed elsewhere and experience certificate in original (if any) need to be produced at the time of interview.
Location of IISR Kozhikode Main Campus - Pallithazham bus stop between Moozhikkal East and Chelavoor on the NH 212 ”Kozhikode - Kollegal” Road.

Advertisement: www.spices.res.in/pdf/DISC-Website.pdf

Converting FASTQ to FASTA

Neel — Fri, 12 Jan 2018 03:49:09 -0600

There are several ways you can convert fastq to fasta sequences. Some methods are listed below.

Using SED

sed can be used to selectively print the desired lines from a file, so if you print the first and 2rd line of every 4 lines, you get the sequence header and sequence needed for fasta format.

sed -n '1~4s/^@/>/p;2~4p' INFILE.fastq > OUTFILE.fasta

Using PASTE

You can linerize every 4 lines in a tabular format and print first and second field using paste

cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr -s "/t" "/n" > OUTFILE.fasta

EMBOSS:seqret

Standard script that can be used for many purposes. One such use is fastq-fasta conversion

seqret -sequence reads.fastq -outseq reads.fasta

awk can be used for conversion as follows:

Using AWK

cat infile.fq | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > file.fa

FASTX-toolkit

fastq_to_fasta is available in the FASTX-toolkit that scales really well with the huge datasets

fastq_to_fasta -h
usage: fastq_to_fasta [-h] [-r] [-n] [-v] [-z] [-i INFILE] [-o OUTFILE]
# Remember to use -Q33 for illumina reads!
version 0.0.6
       [-h]         = This helpful help screen.
       [-r]         = Rename sequence identifiers to numbers.
       [-n]         = keep sequences with unknown (N) nucleotides.
                   Default is to discard such sequences.
       [-v]         = Verbose - report number of sequences.
                   If [-o] is specified,  report will be printed to STDOUT.
                   If [-o] is not specified (and output goes to STDOUT),
                   report will be printed to STDERR.
       [-z]         = Compress output with GZIP.
       [-i INFILE]  = FASTA/Q input file. default is STDIN.
       [-o OUTFILE] = FASTA output file. default is STDOUT.

Bioawk

Another option to convert fastq to fasta format using bioawk

bioawk -c fastx '{print ">"$name"\n"$seq}' input.fastq > output.fasta

Seqtk

From the same developer, there is another option using a tool called seqtk

seqtk seq -a input.fastq > output.fasta

Note that you can use either compressed or uncompressed files for this tool

Senior Research Fellow @ Indian Agricultural Statistics Research Institute

Thu, 23 Jan 2014 06:22:15 -0600

Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi – 110012

Walk-in-Interview

Walk-in-interview will be held on February 11, 2014 at 10:00 A.M. at IASRI, New Delhi for a project “Whole Genome Sequencing and Development of Allied Genomics Resources in Two Commercially Important Fish-Labeo rohita and Clarias batrachus” funded by Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi for the following posts. The appointment will be on contractual basis upto September, 2016 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.

Senior Research Fellow Two

Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application/ Biotechnology or equivalent with 1st Division

 Knowledge of Statistical Analysis /Bioinformatics tools/computer programming for computational genomics.

Emoluments for Research Associate: Consolidated Rs: 16000/- per month + 30% HRA (1st Two years) and Rs: 18000/- per month + 30% HRA (3rd Year)

Age Limit: Age should be not more than 35 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates as on date of interview).
Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph. Original certificates/ Degrees are needed to be produced at the time of interview. No T.A. /D.A. will be paid for appearing in the interview.

Advertisement: http://www.iasri.res.in/employment/2014/srf_cabin.pdf

Frontend: Perl Web framework documentation - Andrej Sali Lab

Jit — Mon, 08 Jan 2018 22:32:03 -0600

The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list of all jobs in the system, and get back job results. The main saliwebfrontend class must be subclassed for each web service. This class is then used to display the web pages using a set of CGI scripts that are set up automatically by the build system.

Address of the bookmark: https://saliweb.readthedocs.io/en/latest/frontend.html

JRF @ Institute of Cytology & Preventive Oncology

Sat, 01 Feb 2014 13:47:29 -0600

Institute of Cytology & Preventive Oncology (ICPO) which was initially established as Cytology Research Centre ( CRC ) by the Indian Council of Medical Research (ICMR) in 1979, came into the existence in 1989 when CRC was elevated to the level of Institute. ICPO was instituted with the main aim of promoting research in the field of cancers that are most prevalent in India with an emphasis on their early detection and prevention.

Candidates having the below mentioned qualifications may appear for Walk in Interview at ICPO on 5th Feb 2014 between 10.00 AM and 12.00 PM under the NIF project entitled "Prediction of drug tragets of chemical constituents present within non-codified medicinal plants" under Dr Subhash M.Agarwal, Scientist C

Position : JRF
No of Post : One
Pay : Rs 12000/- + 30% HRA

Desired Profile : M.Sc in Bioinformatics with good academic record. Candidate with experience in database development and scripting would be preferred
Age Limit : Below 28 years
Period : 2 months

Interested candidates may send their applications with bio-data by email (smagarwal@gmail.com) or post addressed to Dr Subhash M Agarwal, Scientist C, Bioinformatics Division, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector 39, Noida-201301 so as to reach latest by 04.02.14

Deadline : 04.02.14

http://icmr.nic.in/icmrnews/icpo_jrf.pdf

Biotite: A general framework for computational biology

Jit — Mon, 17 Dec 2018 18:52:27 -0600

The package is open source and freely available at GitHub (https://github.com/biotite-dev/biotite). This package is simple to use especially for the beginners in programming and computationally efficient because of the implementation of Numpy and Cython. Biotite consists of four sub packages: sequence, structure, databases, and application. The sequence and structure modules serve for the analysis of sequence and structural data analysis respectively, database downloads files from the other databases such as RCSB PDB, and application provides interface for external software.

The Biotite package bundles popular tasks in computational biology into an unifying framework, which is easy to use on the one hand side, but is also computationally efficient due to intensive usage of NumPy and Cython. This package focuses on working with sequence and structure data and supports various file formats and analysis and manipulation functions.

Address of the bookmark: https://github.com/biotite-dev/biotite

Peng Lab

Tue, 18 Feb 2014 13:53:46 -0600

Peng Lab at Janelia Farm Research Campus, Howard Hughes Medical Institute focuses on data mining for bioinformatics and computational molecular biology, particularly, bioimage data mining and informatics. These bioimages include cellular and molecular images and related medical images.

* Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
* Feature/Model Learning: developing algorithms and software

Location :Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

http://research.janelia.org/peng/

Dash: a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript.

Jit — Tue, 05 Nov 2019 06:39:48 -0600

Dash is a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript.

Dash Bio is a suite of bioinformatics components that make it simpler to analyze and visualize bioinformatics data and interact with them in a Dash application.

The source can be found on GitHub at plotly/dash-bio.

These docs are using Dash Bio version 0.1.4.

Address of the bookmark: https://dash.plot.ly/dash-bio

Assistant Professor @ King Saud University Riyadh

Fri, 21 Feb 2014 05:57:18 -0600

Qualifications: Candidates must have a Ph.D. and a strong background in Molecular and Cellular Biology, protein expression, FACS, or computational biology, and ability to work collaboratively.

This position will have a significant focus on providing analytical support for next generation sequencing data analysis – Exome-sequencing, Targetted sequencing as well as high-throughput genotyping on Illumina platform.

Job location:

Genome Research Chair
King Saud University, Riyadh-11451
KSA

Interested candidate may forward their CV to grcksu@gmail.com