BOL: All Files

Life of a Bioinformatician !

Jitendra Narayan — Fri, 15 May 2026 02:30:08 -0500

Somewhere between FASTQ files, volcano plots, and 3 AM coffee… the gene is probably hiding too.

#Bioinformatics #Genomics #ResearchL

Spades tutorial PDF

Abhimanyu Singh — Tue, 01 Feb 2022 04:56:43 -0600

SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets.

Prepare for Coding Interview !

Abhi — Tue, 11 Jan 2022 06:14:41 -0600

This is a comprehensive guide to prepare for your next coding interview. It's great for recent graduates and has questions and practice materials structured from traditional big tech interview formats.

While it does not include the latest developments in programming since 2019, it nails the core fundamentals in a very comprehensive and accessible way!

Credits to Kaiyu Zhang, with additional material in the appendix sourced from Reddit.

People say that interviews at Google will cover as much ground as possible. As a new college graduate, the ground that I must capture are the following. Part of the list is borrowed from a reddit post: https://www. reddit.com/r/cscareerquestions/comments/206ajq/my_onsite_interview_experience_at_google/ #bottom-comments.

1. Data structures

2. Trees and Graph algorithms

3. Dynamic Programming

4. Recursive algorithms

5. Scheduling algorithms (Greedy)

6. Caching 1

7. Sorting

8. Files

9. Computability

10. Bitwise operators

11. System design

Where to Aproach for R&D Funds in India ?

Surabhi Chaudhary — Thu, 24 Jun 2021 01:04:30 -0500

Companies and governments do research and development (R&D/ R'n'D/ R+D) to promote innovation in order to produce new goods or services and/or enhance existing product lines. R&D covers all actions inside an organization aimed at boosting innovation, such as creating incubators, assisting innovators in scaling up their ideas, and cultivating an innovation culture.

Here are the list of all the research and development funding agencies in India.

DNA RNA MEME

Neel — Thu, 28 Jan 2021 11:23:14 -0600

Explain the DNA and RNA with picture ...

Sample bandage input file for visual analysis

Jit — Wed, 06 Jan 2021 03:51:50 -0600

Sample bandage input file for visual analysis ...

analyzing codon usage

Neel — Thu, 07 Nov 2019 08:31:05 -0600

perl script analyzing codon usage in an input sequence to evaluate how efficiently it will be expressed in Anopheles gambiae. The input codon usage table derived from highly‐expressed A. gambiae genes is appended below.

Biotechnology Eligibility Test (BET) Answer set !

Abhimanyu Singh — Wed, 17 Apr 2019 04:57:58 -0500

DBT-BET JRF 2019 Exam was held successfully on 14th April 2019. Official Question Paper & Answer key of DBT-BET 2019 Exam has been released.

The best part about the DBT-BET Exam is both the question paper & answer key is released immediately after the exam so you get the upper hand here to check how well you did in the DBT-BET exam, how much you are going to score and if you can pass the Exam with good score. This helps you in planning your career ahead.

DBT Exam is held once in a year by Department of Biotechnology – Govt of India. Candidates willing to get DBT-Junior Research Fellowship – DBT JRF fellowship should take up the DBT-BET Exam, DBT – Biotechnology Eligibility Test (BET) 2020 to be held on somewhere in the month of April. Official Notification for DBT-BET 2020 will be released in Feb 2020.

Question at https://bioinformaticsonline.com/file/view/39260/biotechnology-eligibility-test-bet-question-paper

Biotechnology Eligibility Test (BET) Question Paper !

Abhimanyu Singh — Wed, 17 Apr 2019 04:56:33 -0500

DBT-BET JRF 2019 Exam was held successfully on 14th April 2019. Official Question Paper & Answer key of DBT-BET 2019 Exam has been released.

Answer at https://bioinformaticsonline.com/file/view/39262/biotechnology-eligibility-test-bet-answer-set

Evaluation of genome assembly software based on long reads

BioStar — Fri, 01 Feb 2019 11:55:54 -0600

TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing analyses, to create detailed maps of structural variations in many species. Also, these new technologies have been used to fill in many of the gaps in the human reference genome.

In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads