• New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
• New export function for BAM/cSRA coverage graphs (Tutorial)
• New export function for alignments GFF3 format ((Tutorial))
• Tree View: implemented new export mode based on selections (tutorial coming)
• Tree View: added support for distance based circular trees
• Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
• Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)

ORFfinder is a graphical analysis tool for finding open reading frames (ORFs). We’ve been working on a few updates, and we’d like to find out what you think about them. Read on to find out what you can do with the new ORFfinder.

Smart BLAST (https://ncbiinsights.ncbi.nlm.nih.gov/2015/07/29/smartblast/)

Select one or a group of ORFs and BLAST several databases at once, and use the newly developed SmartBLAST to verify protein names. Looking for the traditional results from BLAST? They’re there too.

• Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
• Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
• Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
• GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
• Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
• Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
• Open Source: Prodigal source code is freely available under the General Public License.

Address of the bookmark: http://prodigal.ornl.gov/

The purpose of the hive plot is to establish a new baseline for visualization of large networks — a method that is both general and tunable and useful as a starting point in visually exploring network structure.

More at http://www.hiveplot.com/

Address of the bookmark: http://www.hiveplot.com/

More at https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leidosbiomed&id=2040

No of vacancies: 01

Pay scale:Rs. 15600 – 39100 + 6600/-

Essential Academic Qualifications / Experience : Good academic record as defined by the concerned university with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master's Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university.

Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/ SET.

Notwithstanding anything contained in sub-clauses (a) and (b) to this Clause, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.

NET/SLET/SET shall also not be required for such Masters Programmes in disciplines for which NET/SLET/SET is not conducted.

Apply online: http://www.psc.cg.gov.in/htm/OA_ME2014.html

Last Date for Online Registration: 22/05/2014

For more details: http://www.psc.cg.gov.in/pdf/Advertisement/ADV_ME2014.pdf

Why Bioinformatics Matters More Than Ever

Every day, our world generates massive amounts of biological data—from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.

Bioinformatics isn’t just a skill.
It’s the language of the future of biology.

By mastering it, you give yourself the power to:

Decode genomes and understand life at its most fundamental level

Identify patterns no microscope could ever reveal

Predict disease outbreaks before they occur

Accelerate drug discovery with computational precision

Contribute to open-source tools that empower scientists worldwide

You don’t just follow science—you drive it.

Every Expert Was Once a Beginner

Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.

But here’s the truth: every bioinformatician started exactly where you are now—curious, unsure, but excited.

No one writes perfect code on day one.

No one understands genomics pipelines immediately.

What makes you a bioinformatician is not perfection, but perseverance.

When your script throws a cryptic error…
When your data refuses to format…
When your pipeline runs for 6 hours only to crash…

Remember: this is part of the journey.
Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.

Bioinformatics Is Not Just a Career—It’s a Mindset

It’s the mindset of:

Problem-solving.

Continuous learning.

Turning chaos into clarity.

Seeing what others can’t.

Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.

Your Contribution Matters

As you work on your script, pipeline, genome, or model, remember:

Somewhere, your analysis might contribute to:

A new therapy

A faster diagnostic test

A better understanding of a pathogen

A more resilient crop

An open-source dataset that helps thousands

A discovery that rewrites textbooks

Your code may be small, but its ripple effect is powerful.

The Future Is Bioinformatics—And You Are Part of It

The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.

This is a golden era—and you are not late.
You are exactly where you need to be.

Keep Pushing. Keep Learning. Keep Discovering.

Bioinformatics is a journey filled with challenges, but also with unmatched rewards.

So the next time you feel stuck, frustrated, or overwhelmed, remember:
You’re building the science of tomorrow.

Be proud. Stay curious. Keep going.
Your work matters more than you think.

Following are the list of resource and location for TE discovery and TE detection:

BLASTER suite http://urgi.versailles.inra.fr/development/blaster/ 

Censor http://www.girinst.org/censor/download.php 

find_ltr http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl 

FINDMITE http://jaketu.biochem.vt.edu/dl_software.htm

HMMER http://hmmer.janelia.org/

LTR_FINDER http://tlife.fudan.edu.cn/ltr_finder/

LTR_STRUC http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html

LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7

LTR_par http://www.eecs.wsu.edu/~ananth/software.htm

MAK http://wesslercluster.plantbio.uga.edu/mak06.html

MaskerAid http://blast.wustl.edu/maskeraid/

mer-engine http://mer-engine.cshl.edu/mer-home.php

mreps http://bioinfo.lifl.fr/mreps/

PILER http://www.drive5.com/piler/

PLOTREP http://repeats.abc.hu/cgi-bin/plotrep.pl

RepBase http://www.girinst.org/

RepeatFinder http://cbcb.umd.edu/software/RepeatFinder/

RepeatGluer http://nbcr.sdsc.edu/euler/intro_tmp.htm

RepeatMasker http://www.repeatmasker.org/

RepeatRunner http://www.yandell-lab.org/repeat_runner/index.html

RepeatScout http://repeatscout.bioprojects.org/

repeat-match http://mummer.sourceforge.net/

REPuter http://www.genomes.de/

RetroMap http://www.burchsite.com/bioi/RetroMapHome.html

SMaRTFinder http://bioinf.dimi.uniud.it/software/software/smartfinder

Tandem Repeats Finder http://tandem.bu.edu/trf/trf.html

Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html

TE nest http://www.plantgdb.org/prj/TE_nest/TE_nest.html

TRANSPO http://alggen.lsi.upc.es/recerca/search/transpo/transpo.html

TSDfinder http://www.ncbi.nlm.nih.gov/CBBresearch/Landsman/TSDfinder/

Tu Lab TE tools http://jaketu.biochem.vt.edu/dl_software.htm

WU-BLAST http://blast.wustl.edu

More at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369

Address of the bookmark: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000369