BOL: Related items

BioKit: a set of tools dedicated to bioinformatics, data visualisation

Neel — Tue, 18 Jun 2024 02:04:39 -0500

BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g., biokit.stats). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html

Associate Professor - Bio-Informatics at University of Allahabad in Allahabad

Wed, 07 May 2014 00:26:53 -0500

No of vacancies: 01

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

Perl Special Vars Quick Reference

Abhimanyu Singh — Tue, 07 Feb 2017 05:08:47 -0600

`$_`	The default or implicit variable.
`@_`	Subroutine parameters.
`$a` `$b`	sort comparison routine variables.
`@ARGV`	The command-line args.
Regular Expressions
`$`	Regexp parenthetical capture holders.
`$&`	Last successful match (degrades performance).
`${^MATCH}`	Similar to `$&` without performance penalty. Requires /p modifier.
$`	Prematch for last successful match string (degrades performance).
`${^PREMATCH}`	Similar to $` without performance penalty. Requires `/p` modifier.
`$'`	Postmatch for last successful match string (degrades performance).
`${^POSTMATCH}`	Similar to `$'` without performance penalty. Requires `/p` modifier.
`$+`	Last paren match.
`$^N`	Last closed paren match (last submatch).
`@+`	Offsets of ends of successful submatches in scope.
`@-`	Offsets of starts of successful submatches in scope.
`%+`	Like `@+`, but for named submatches.
`%-`	Like `@-`, but for named submatches.
`$^R`	Last regexp (?{code}) result.
`${^RE_DEBUG_FLAGS}`	Current value of regexp debugging flags. See `use re 'debug';`
`${^RE_TRIE_MAXBUF}`	Control memory allocations for RE optimizations for large alternations.
Encoding
`${^ENCODING}`	The object reference to the Encode object, used to convert the source code to Unicode.
`${^OPEN}`	Internal use: \0 separated Input / Output layer information.
`${^UNICODE}`	Read-only Unicode settings.
`${^UTF8CACHE}`	State of the internal UTF-8 offset caching code.
`${^UTF8LOCALE}`	Indicates whether UTF8 locale was detected at startup.
IO and Separators
`$.`	Current line number (or record number) of most recent filehandle.
`$/`	Input record separator.
`$\|`	Output autoflush. 1=autoflush, 0=default. Applies to currently selected handle.
`$,`	Output field separator (lists)
`$\`	Output record separator.
`$"`	Output list separator. (interpolated lists)
`$;`	Subscript separator. (Use a real multidimensional array instead.)
Formats
`$%`	Page number for currently selected output channel.
`$=`	Current page length.
`$-`	Number of lines left on page.
`$~`	Format name.
`$^`	Name of top-of-page format.
`$:`	Format line break characters
`$^L`	Form feed (default "\f").
`$^A`	Format Accumulator
Status Reporting
`$?`	Child error. Status code of most recent system call or pipe.
`$!`	Operating System Error. (What just went 'bang'?)
`%!`	Error number hash
`$^E`	Extended Operating System Error (Extra error explanation).
`$@`	Eval error.
`${^CHILD_ERROR_NATIVE}`	Native status returned by the last pipe close, backtick (`` ) command, successful call to wait() or waitpid(), or from the system() operator.
ID's and Process Information
`$$`	Process ID
`$<`	Real user id of process.
`$>`	Effective user id of process.
`$(`	Real group id of process.
`$)`	Effective group id of process.
`$0`	Program name.
`$^O`	Operating System name.
Perl Status Info
`$]`	Old: Version and patch number of perl interpreter. Deprecated.
`$^C`	Current value of flag associated with -c switch.
`$^D`	Current value of debugging flags
`$^F`	Maximum system file descriptor.
`$^I`	Value of the -i (inplace edit) switch.
`$^M`	Emergency Memory pool.
`$^P`	Internal variable for debugging support.
`$^R`	Last regexp (?{code}) result.
`$^S`	Exceptions being caught. (eval)
`$^T`	Base time of program start.
`$^V`	Perl version.
`$^W`	Status of -w switch
`${^WARNING_BITS}`	Current set of warning checks enabled by `use warnings;`
`$^X`	Perl executable name.
`${^GLOBAL_PHASE}`	Current phase of the Perl interpreter.
`$^H`	Internal use only: Hook into Lexical Scoping.
`%^H`	Internaluse only: Useful to implement scoped pragmas.
`${^TAINT}`	Taint mode read-only flag.
`${^WIN32_SLOPPY_STAT}`	If true on Windows `stat()` won't try to open the file.
Command Line Args
`ARGV`	Filehandle iterates over files from command line (see also `<>`).
`$ARGV`	Name of current file when reading <>
`@ARGV`	List of command line args.
`ARGVOUT`	Output filehandle for -i switch
Miscellaneous
`@F`	Autosplit (-a mode) recipient.
`@INC`	List of library paths.
`%INC`	Keys are filenames, values are paths to modules included via `use, require,` or `do`.
`%ENV`	Hash containing current environment variables
`%SIG`	Signal handlers.
`$[`	Array and substr first element (Deprecated!).

See perlvar for detailed descriptions of each of these (and a few more) special variables.

DNA Replication Process [3D Animation]

Sat, 10 May 2014 04:41:22 -0500

See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Jit — Fri, 08 Dec 2017 16:48:40 -0600

Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to Tom Slezak for revsing the get_genbank_file3 script and to Tod Stuber (USDA) for testing version 3.1 even though he doesn't need the annotation feature. All users are encouraged to upgrade to version 3.1.

Address of the bookmark: https://sourceforge.net/projects/ksnp/files/

Bioinformatics PhD at CUK Kerala

Sat, 10 May 2014 20:21:22 -0500

Applications are invited from highly motivated students (UGC-CSIR-JRF) with a background in Genomics/ Biotechnology/ Molecular Microbiology/ Biochemistry and Bioinformatics to pursue research leading to Ph.D. in the following areas;

1. Cancer Genomics

2. Microbial Genetics and Metagenomics

3. Human Infective Diseases

4. Computational Drug Design

Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor & Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com

assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference genome

Jit — Thu, 14 Jun 2018 07:31:00 -0500

Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X faster) $ gzip OUT.delta Then use the OUT.delta.gz file for upload. Upload the .delta or delta.gz file (view example) to Assemblytics Important: Use only contigs rather than scaffolds from the assembly. This will prevent false positives when the number of Ns in the scaffolded sequence does not match perfectly to the distance in the reference. The unique sequence length required represents an anchor for determining if a sequence is unique enough to safely call variants from, which is an alternative to the mapping quality filter for read alignment. http://assemblytics.com/

Address of the bookmark: http://assemblytics.com/

A Brief Bioinformatics Tutorial

Jit — Wed, 21 May 2014 12:50:09 -0500

This is about how to use a computer to find what is known about a gene of interest and also how to get new insights about it.

The tutorial is divided in three main parts:

In the Sequence part, you will see how to look efficiently for a particular protein sequence, how to blast it against the database of your choice to find homologues, how to perform a multiple alignment of the homologues you've selected and how to edit this alignment.
The Structure part is about molecular visualization, homology modeling and structural domain prediction.
In the Function part, you will be introduced to you 3 useful servers to investigate the function of a protein. i.e. finding interactors, co-expressed genes, see a phylogenetic profile, easily access papers citing your gene etc ...

During all the three parts, we will use the S. cerevisiae VPS36 protein as an example.

Address of the bookmark: http://www.mrc-lmb.cam.ac.uk/rlw/text/bioinfo_tuto/introduction.html

Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism

Rahul Nayak — Sun, 23 Feb 2020 02:17:30 -0600

MCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples. To provide easy access to these sequences, we recently added a separate rRNA/ITS databases section on the nucleotide BLAST page for these targeted sequences that makes it convenient to quickly identify source organisms. The new databases are:

*16S ribosomal RNA (Bacteria and Archaea)

*18S ribosomal RNA sequences (SSU) from Fungi type and reference material

*28S ribosomal RNA sequences (LSU) from Fungi type and reference material

*Internal transcribed spacer region (ITS) from Fungi type and reference material

You can also download these from the BLAST db FTP area. See the NCBI Insights post for more detail.

Useful links

-----------------

BLAST form with rRNA/ITS databases

BLAST db download

Targeted loci

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

Bioinformatics JRF/SRF position at NII

Sun, 25 May 2014 16:54:04 -0500

NATIONAL INSTITUTE OF IMMUNOLOGY, NEW DELHI-110067

Applications are invited for the position of Senior Research Fellow for the following time-bound sponsored project as per the details given below:

1. BTIS project on, “Bioinformatics Center-National Infrastructural Facility in the Area of Immunology” funded by DBT

Senior Research Fellow (P) (One Position only)

Dr. Debasisa Mohanty
Staff Scientist-VI
deb@nii.res.in

Qualifications: M.Sc in Biological Sciences or Biotechnology with at least 04 years of Research experience in Bioinformatics or computational Biology after the master’s degree is essential.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience

Rs. 18,000/- per month consolidated plus 30% HRA if Leading to Ph.D/NET/GATE Qualified otherwise Rs. 14,000/- per month + 30% HRA.

Job description: The candidate should be well versed in programming in PERL/C++/HTML/CGI, web server and portal development, computational analysis of
protein structure & function, molecular dynamics simulations and use of high performance computing systems.

GENERAL TERMS AND CONDITIONS:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.
2. No hostel/ housing facility will be provided.
3. Number of posts may vary and shall be need based. Advertisement is no commitment.
4. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.
5. No TA/DA will be paid for attending the interview, if called for.
6. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., e-mail id, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC / ST and PH candidates are exempted subject to submission of documentary proof), at the time of interview.

LAST DATE OF RECEIPT OF APPLICATIONS: 06th June, 2014

www1.nii.res.in/sites/default/files/projectappointment-Dr.Mohanty-6June2014.pdf