<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26993?offset=1220 https://bioinformaticsonline.com/bookmarks/view/43658/uniquekmer-generate-unique-kmers-for-every-contig-in-a-fasta-file Fri, 17 Dec 2021 00:08:15 -0600 https://bioinformaticsonline.com/bookmarks/view/43658/uniquekmer-generate-unique-kmers-for-every-contig-in-a-fasta-file <![CDATA[UniqueKmer: Generate unique KMERs for every contig in a FASTA file]]> Generate unique k-mers for every contig in a FASTA file.

Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands).

This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers for each contig.

The output unique k-mer file and Genome file can be used for fastv: https://github.com/OpenGene/fastv, which is an ultra-fast tool to identify and visualize microbial sequences from sequencing data.

https://github.com/OpenGene/UniqueKMER

Address of the bookmark: https://github.com/OpenGene/UniqueKMER

]]> Abhi https://bioinformaticsonline.com/opportunity/view/22072/bioinformatics-jrfrasrf-position-at-indian-institute-of-science-education-and-research-iiser-kolkata-kolkata-west-bengal Fri, 17 Apr 2015 04:11:14 -0500 <![CDATA[Bioinformatics JRF/RA/SRF position at Indian Institute of Science Education and Research (IISER Kolkata) - Kolkata, West Bengal]]> Research Position in Computational Biology in the group of Shree P. Pandey Positions available in the area of NGS data analysis, bioinformatics, plant genomics

Project Description: Projects involves high throughput analysis of data mostly generated by massively parallel sequencing (RNA-Seq and small-RNA-Seq), microarrays and related platforms. We are looking for highly motivated and bright individuals interested in high-throughput cutting-edge data analyses methods in genomics (computational positions). Available positions: Applications are invited from suitable candidates in both, the Max Planck India Partner Program and the CRP Wheat Program for openings at the levels:

Post Name-Qualification-Salary:
Project assistant – Master’s – Rs. 14000
Project fellow (junior data analyst) – Masters + research experience – Rs. 16000
Research fellow (senior data analyst) – Masters + adequate research experience/desirable skill sets – Rs. 22000
Research Associated – PhD (< 1yr) /> 1 yr experience – Rs. 28000 / Rs. 32000
Essential qualification: MSc/MTech/PhD (or other suitable qualification) in discipline related to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance Post-Graduate Diploma in Bioinformatics’. Proficiency in one of the programming languages or statistics (proficient in R for example) is compulsory.
Desirable qualification: 1. Programming experiences in at least one low level language such as C/C++ and one scripting language such as Perl/Python/PHP and knowledge of SQL/MySQL. 2. Substantial experience in the linux or other unix environments. 3. Experience of working in projects on Bioinformatics, Genetics or Biological application areas/Computational and Statistical analysis (e.g. using R or Matlab). Experience in the field of genomics (NGS, microarrays, genome annotation), database development and management, software development, systems and network biology (or related fields) will be preferred.
SELECTION PROCEDURE FOR INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH (IISER KOLKATA) – RESEARCH ASSOCIATE & MORE VACANCIES POST:

Candidates can apply on or before 30/04/2015
No Detailed information about the selection process is mentioned in the recruitment notification
HOW TO APPLY FOR RESEARCH ASSOCIATE & MORE VACANCIES IN INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH (IISER KOLKATA):

Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by email to Shree P. Pandey, Department of Biological Sciences, IISER-Kolkata, Mohanpur Campus, West Bengal within 2 weeks. Interviews will be scheduled within 10 days of closing of applications. E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in
For more details visit: http://www.iiserkol.ac.in/~sppandey

]]> https://bioinformaticsonline.com/bookmarks/view/43799/kast Wed, 23 Feb 2022 08:28:36 -0600 https://bioinformaticsonline.com/bookmarks/view/43799/kast <![CDATA[KAST]]> Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

Address of the bookmark: https://github.com/martinjvickers/KAST

]]> Neel https://bioinformaticsonline.com/opportunity/view/22235/project-fellow-bioinformatics-at-central-drug-research-institute Mon, 27 Apr 2015 20:15:45 -0500 <![CDATA[Project Fellow Bioinformatics at Central Drug Research Institute]]> Project Fellow (Bioinformatics)
Central Drug Research Institute
Address: Chattar Manzil, M.G.Road, Kaisarbagh
Postal Code: 226001
City: Lucknow
State: Uttar Pradesh
Pay Scale: Rs.16,000/- (fixed) p.m.
Educational Requirements: M.Sc. in Bioinformatics with 55% marks for Gen. & OBC and 50% marks for SC/ST candidates, Physically and Visually handicapped candidates
Experience Requirements: Experience in computer-assisted scientific research in the area of Drug Design including Bio- molecular modeling and simulation studies, Virtual screening, pharmacophore perception, QSAR etc. Familiarity with Linux/Unixbased computer systems and required to participate and contribute to the development and application of computational models for the design and discovery of novel molecules as inhibitors or chemical probes
Details will be available at: http://cdriindia.org/uploaded/advt_no01-2015.pdf

How To Apply: Eligible candidates required to report for the Interview at 9:00 A.M. sharp on 11-05-2015 (For Position Code No. 001 to 009) and 12-05-2015 (For Position Code No. 010 to 016). Candidates reporting after 10:00 A.M will not be allowed to attend the interview. Eligible candidates may appear before the Selection Committee for interview on the date and time mentioned above at CDRI, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow-226031. Eligible candidates must bring with them duly filled up application form (which can be downloaded from our website www.cdriindia.org), along with Original certificates as well as attested copies of certificates of examinations starting from matriculation, date of birth, caste certificate (in case of SC/ST/OBC) experience certificate, publication, if any and recent passport size photograph etc. Original documents are essential for verification of the particulars quoted by the candidate in the application form and candidate failed to produce original documents at the time of verification, shall not be allowed to attend the interview. Any request for relaxation in this regard shall not be entertained.
Detail of Interview: 11-05-2015
Age Limit: 28 Years

]]> https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator Wed, 08 Mar 2023 01:39:33 -0600 https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator <![CDATA[ALE: Assembly Likelihood Estimator]]> Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly.  Depending on your genome size you may want to convert the .wig files to the BigWig format.

Address of the bookmark: https://github.com/sc932/ALE

]]> BioStar https://bioinformaticsonline.com/opportunity/view/22269/school-of-life-sciences-jawaharlal-nehru-university-vacancy-of-jrf-srf-ra-in-csir-funded-project Wed, 29 Apr 2015 21:26:19 -0500 <![CDATA[School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Project]]> School of Life Sciences, Jawaharlal Nehru University has issued notification dated 27.04.2015 to fill the vacancy of JRF / SRF / RA in CSIR funded Projec entitled "Structural and functional characterization of serine biosynthetic pathway enzymes from entamoeba histolytica". It is good chance to get job with IITKGP and brighten your future. Learn eligibility criteria and apply on or before 08.05.2015.

Employer: Jawaharlal Nehru University
Address: Dr. S. Gourinath, Principal Investigator, School Of Life Sciences, Jawaharlal Nehru University, New Delhi-110067
Email: not mentioned / provided for this job post
URL: http://www.jnu.ac.in/Career/currentjobs.htm
Phone: 011 2674 2575
Skills: not mentioned / required for this job post
Experience: Experience in molecular biology, structural biology and bioinformatics is desired
Education: M.Sc. in any field of life sciences.
Job Location: New Delhi, Delhi, India (View Jobs in New Delhi, Jobs in Delhi, Jobs in India)

Job Description: School of Life Sciences, Jawaharlal Nehru University vacancy of JRF / SRF / RA in CSIR funded Projec

Name of the Post: JRF / SRF / RA

Salary: As per rules

Required Job Profile:

Candidate must possess M.Sc. in any field of life sciences.

Desired Job Profile:

Candidate having NET - CSIR or UGC and experience in molecular biology, structural biology and bioinformatics is desired and experience with publication is preferred.

How to apply:

Eligible and interested candidates should need to apply with complete details to the above mentioned address on or before 08.05.2015.

Refer to http://www.jnu.ac.in/Career/currentjobs.htm

]]> https://bioinformaticsonline.com/pages/view/44371/steps-to-find-all-the-repeats-in-the-genome Thu, 31 Aug 2023 02:43:28 -0500 https://bioinformaticsonline.com/pages/view/44371/steps-to-find-all-the-repeats-in-the-genome <![CDATA[Steps to find all the repeats in the genome !]]>

To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option[0]. Here's a step-by-step guide:

  1. Install RepeatMasker: First, you need to install RepeatMasker on your system. You can download it from the RepeatMasker website[0].
  1. Prepare the genome sequence: Make sure you have the genome sequence in a FASTA file format. Let's assume the file is named "genome.fasta".

./RepeatMasker -pa <number_of_processors> -nolow -norna -no_is -div <divergence_value> -lib RepeatMaskerLib.embl -gff -xsmall -small -poly -species <species_name> -dir <output_directory> -length <min_length>-<max_length> genome.fasta

Replace the following placeholders with appropriate values:

  • <number_of_processors>: The number of processors/threads you want to use for parallel processing.
  • <divergence_value>: The divergence value for the species you are analyzing. You can find divergence values for different species in the RepeatMasker documentation[0].
  • <species_name>: The name of the species you are analyzing.
  • <output_directory>: The directory where you want the output files to be saved.
  • <min_length> and <max_length>: The minimum and maximum lengths of the repeats you want to find (in this case, 2 and 9).
  1. Analyze the output: RepeatMasker will generate several output files, including a .out file. You can parse this file to extract the information you need. There is a Perl tool called "one_code_to_find_them_all.pl" that can help you parse RepeatMasker output files[0]. You can download it from the source provided.
  1. Use the provided Perl script: Once you have the "one_code_to_find_them_all.pl" script, you can run it to conveniently parse the RepeatMasker output files. Here's an example of how to use it:

perl one_code_to_find_them_all.pl --rm <RepeatMasker_out_file> --length <length_file>

 

Replace <RepeatMasker_out_file> with the path to your RepeatMasker .out file, and <length_file> with the path to a file containing the lengths of the reference elements.

This script will generate several output files, including .log.txt and .copynumber.csv, which contain quantitative information about the identified repeat elements.

Remember to adjust the parameters and options according to your specific needs and the characteristics of your genome.

]]> Neel https://bioinformaticsonline.com/opportunity/view/22297/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics Fri, 08 May 2015 00:24:20 -0500 <![CDATA[Appointment of two traineeships and two studentships in Bioinformatics]]> Applications are invited for the appointment of two traineeships and two studentships in Bioinformatics for a period of six months sponsored by Department of Biotechnology, Government of India in the Bioinformatics Sub-DIC, Saraswathy Thangavelu Centre, JNTBGRI, Puthenthope, Thiruvananthapuram 695 586. The required qualifications and other details are given below.

Position 1: Traineeship
Monthly fellowship (in rupee): 5,000/-
No. of vacancies: Two
Required Qualification: First Class M.Sc Bioinformatics/ Biotechnology/ Botany

Position 2: Studentship
Monthly fellowship (in rupee): 5,000/-
No. of vacancies: Two
Required Qualification: M.Phil/M.Tech Bioinformatics/ Biotechnology/ any branch of Life Science students for doing their thesis work in the area of Bioinformatics.

Age limit as on 1.1.2015, 28 years. Age relaxation will be provided for SC, ST, OBC candidates as per Govt. norms.

Interested candidates may appear for walk-in-interview on 15th May 2015 at 10.30 am at JNTBGRI, Palode, Thiruvananthapuram. The candidate should report to the Office at Palode before 10.00 am.

More at http://jntbgri.res.in/news/appointment-of-two-traineeships-and-two-studentships-in-bioinformatics/

]]> https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome Thu, 08 Aug 2024 23:31:18 -0500 https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome <![CDATA[Tools to access the quality of your assembled genome !]]>
  • FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
  • GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
  • ASSEMBLATHON STATS: Assembly statistics
  • GENOMETOOLS GT STAT: Annotation statistics
  • NCBI FCS ADAPTOR: Adaptor contamination pass/fail
  • NCBI FCS GX: Foreign organism contamination pass/fail
  • BUSCO: Gene-space completeness estimation
  • TIDK: Telomere repeat identification
  • LAI: Continuity of repetitive sequences
  • KRAKEN2: Taxonomy classification
  • HIC CONTACT MAP: Alignment and visualisation of HiC data
  • MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
  • MERQURY: K-mer completeness, consensus quality and phasing assessment
    • ]]>     LEGE     https://bioinformaticsonline.com/researchlabs/view/22393/narcis-fernandez-fuentes-lab Mon, 25 May 2015 07:30:00 -0500 <![CDATA[Narcis Fernandez-Fuentes Lab]]> Welcome to our web-site compiling all the research-related activities of the group. Our research interests relate to a number of areas within Bioinformatics. We have a long-standing interest in protein structure prediction and structure-to-function relationships. We work in the study of biomolecular interactions, modeling of protein complexes, the study and characterization of protein-protein interactions, peptide design, modeling of genetic variation, structure-based protein design and different aspects of Plant Bioinformatics. Take a look at the our databases and servers and the list of publications for more information.

    More at http://www.bioinsilico.org/

    ]]>