Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

LPI scores are inversely proportional to the phylogenetic distance between database match sequences and the query genome. These scores are useful not only for large-scalede novo predictions of horizontally transferred proteins, but can also serve as an independent quality control test for potential horizontal transfer candidates identified by alternative methods, especially those based on nucleic acid signatures. Candidates having high LPI scores are unlikely to have been horizontally transferred, since they are highly conserved among closely related organisms.

One unique and powerful feature of the DarkHorse HGT Candidate database is the opportunity to explore the phylogenetic background of potential HGT donors as well as recipients. The breadth of the database allows not only query sequences, but also their database match partners to be evaluated for sequence similarity or novelty compared to taxonomically related organisms.

DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A brief tutorial page is also available on-line.

Address of the bookmark: http://darkhorse.ucsd.edu/download.html

This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties.

To decode a given SAM flag value, just enter the number in the field below. The encoded properties will be listed under Summary below, to the right.

Address of the bookmark: https://broadinstitute.github.io/picard/explain-flags.html

Currently CSBB provides 13 modules focused on analytical tasks like performing upper-quantile normalization on expression data or convert genome wide gene expression to z-scores when comparing expression data from different platforms.

More at https://github.com/skygenomics/CSBB-v1.0

Address of the bookmark: https://github.com/skygenomics/CSBB-v1.0

These are just a scant few of the common questions asked by bioinformatics students as they ready themselves for the next exam sitting. If you read the entire Syllabus (and I know that everyone does), you will see a section devoted to study and exam techniques. The section discusses such broad concepts as motivation, scheduling, and retention. Upon reading this section, however, I find the "hints" to be too general. Much of the advice boils down to read, study, understand, and memorize the material. The techniques mentioned apply to everyone and thus the overall advice ends up as a broad overview of the learning process.

The idea behind this article is to give students ideas on different approaches and techniques in the preparation for exams. By providing various ways to prepare for the exam process, fascinated readers may gain some additional insight to help complement their studying methodology. There are, of course, many common themes expressed in this small empirical sample of students' study habits. The idea of note cards, memorization, and problem solving are frequently mentioned by all students. No matter what technique a candidate uses, it always takes a significant amount of time and personal resources to successfully complete the examination process.

1 Explain it in your own word

Your teacher or lecturer can explain something to you, you can learn it from a text book, your friends can study with you, even your own notes can explain it to you but all these explanations are of little use if, by the end, you can’t explain what you have learned to yourself. The BINC exam looking for ability to write and explain the concept in your own word. You, therefore, need to illustrate in an exam to get top exam results, then you won’t be happy with your end exam result. So don’t just memorise and tick off the list – make sure you understand your theory.

2 Be an examiner yourself

Of course, depending on what you’re studying, it may be quite difficult to get into a position to understand a concept, theory or other information you need to learn. Ask ‘stupid’ question to yourself and train yourself for the worst! Embrace your curiosity, for as William Arthur Ward said: “Curiosity is the wick in the candle of learning.” Doing so will allow you to fill in the blanks and better prepare you for exams.

3 Quiz yourself

Once you feel you understand topic, it is important to test yourself regularly. Try yourself to replicate exam conditions as much as possible: turn your phone off, don’t talk, time yourself etc. You can set yourself a study quiz or practice exam questions and, so long as you approach it with the right mindset, you can get a very good idea of how much you know. You gain a greater insight into where you stand in relation to what you’ve studied so far.

4 Online study

Keeping the fact that, bioinformatics is ever changing subject, you might need to update yourself on timely basis. Don’t feel obliged to just sit in front of a book with a highlighter; there are many different ways to improve your bioinformatics knowledge. Login and check almost all web servers and keep yourself updated, like how many genomes sequenced, sizes, techniques used, software names etc.

5 Study plan

In order to achieve exam success, you need to know what you want to achieve and focus on. That’s why it is extremely important to set your Study Goals now and outline to yourself what you need to do. With your study goals in mind, you properly need to attention all subjects. It should be broad enough to allow you to add and change aspects but concise enough so you know you’re covering each subject/topic as best you can at this point.

Main features:

1. works with any number of scaffold assemblies in de-novo non-progressive fashion
2. allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
3. creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
4. constructs a merged combined scaffold assembly
5. provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

Find out more on our blog:
http://www.ensembl.info/…/find-predicted-crispr-sites-usin…/