Bioinformatics careers: Bioinformatics Systems Analyst Job Offer

Bioinformatics careers: Bioinformatics Systems Analyst Job Offer

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has a job offer for an experienced Bioinformatics Analyst to support the Plant Genome Assembly Analytics Group.

The main responsibility includes obtaining Genomes data and analyzing it using several software, storing and organizing it...etc

For more info about this offer (job requirements and how to apply) you can visit this link HERE.

Bioinformatics: NCBI releases a Database of Genomic Structural Variation (dbVar)

Bioinformatics: NCBI releases a Database of Genomic Structural Variation (dbVar)

As part of NCBI, a new database was released, this database is the Database of Genomic Structural Variation (dbVar), this database contains data from the analysis of genomic variations and their relationship with phenotype information.

The dbVar homepage contains links that help you understand what Genomic Structural Variations are, FAQs, and submission of information.

The database also include an RSS feed to let you know about any updates.

Bioinformatics: Job Offer at University of Copenhagen

The Center for non-coding RNA in Technology and Health at Bioinformatics Faculty of Life Sciences, University of Copenhagen in Denmark, is a newly established center that specialized in studying non-coding RNAs. The center has a position as PhD fellow in bioinformatics open, with start May 1st or soon thereafter. The duration is three years.

This project concentrates on studying ncRNAs or non-coding RNAs, their role, structure...etc

The project will be in collaboration with Prof. Henrik Nielsen, University of Copenhagen and others.

For more on the job description and Qualification requirements, you can read the full article HERE.

Bioinformatics: Protein sequence databases names for use with BLAST

Bioinformatics: Protein sequence databases names for use with BLAST

In the "Nucleotide sequence databases names for use with BLAST" post, we've seen the nucleotide sequence databases names that we can use in a command line BLAST search, the same thing applies to Protein sequence databases when it come to use command line BLAST.

Here are some of the protein databases names that we can use with BLAST:

1- nr:  Non-redundant merge of SWISS-PROT, PIR, PRF, and proteins derived from GenBank coding sequences and PDB atomic coordinates

2- swissprot:  The SWISS-PROT database

3- pdb:  Amino acid sequences parsed from atomic coordinates of three-dimensional structures

4- ecoli:  All proteins encoded by the E. coli genome

5- yeast:  All proteins encoded by the S. cerevisiae genome

6- drosoph: All proteins encoded by the D. melanogaster genome

These are some of the abbreviations used in a commend line BLAST search, if you want more you can read the documentation of using command line BLAST on the internet.


As a Bioinformatician, learning to use command line BLAST on Linux is very important, because it will make parsing files and looking for specific info very easy, because what takes 1 minute in an automated task, will take half an our doing it by hand, and the number goes with the amount of data you want to retrieve.

Any questions, you're welcome:-).

Bioinformatics: video tutorial: Using PHYLIP to build phylogenetic trees

Bioinformatics: video tutorial: Using PHYLIP to build phylogenetic trees

As you know PHYLIP or (PHYlogeny Inference Package) is a set of programs that can construct phylogenetic trees.


To understand what phylogenetic trees can do for you you can read this post HERE.

In order to build phylogenetic trees you have to prepare a set of sequences in a multiple sequence alignment.

In this video tutorial i'm going to use one of the 3 methods in building phylogenetic trees, which is distance methods by using a program included in PHYLIP called protdist.

This video tutorial have 2 parts:

Part 1:



Part 2:



Any questions, comment

Bioinformatics: Nucleotide sequence databases names for use with BLAST

Bioinformatics: Nucleotide sequence databases names for use with BLAST

In most cases people like to use BLAST that is hosted on servers like NCBI, but sometimes you would like to use a command line BLAST already installed on your computer on a Windows or Linux operating system.

In order to do that you have to know the databases names that you can use in the command line BLAST.

Here are some of the nucleotide databases names that you can use with BLAST:

1- nr : Nonredundant GenBank, a database that provides comprehensive collections of both amino acid and nucleotide sequence data, with redundancy reduced by merging sequences that are completely identical.

2- est :  expressed sequence tags.

3- sts : sequence tagged sites.

4- htgs : high-throughput genomic sequences.

5- ecoli : Complete genomic sequence of E. coli.

6- yeast : Complete genomic sequence of S. cerevisiae.

7- drosoph : Complete genomic sequence of D. melanogaster.

8- mito : Complete genomic sequences of vertebrate mitochondria.

9- vector : Collection of popular cloning vectors.

These are some of the most used nucleotide databases names in a BLAST search.

This is an example of a BLAST command:

blastall -i blast.in -d nr -o blast.out

blastall: program name.

-i : input.

blast.in & blast.out : input and output file containing the sequence.

-d : database.

nr : Nonredundant.

You can read (using BLAST to search for similarities) post to learn how to run a BLAST search against a database.

You can read (Different Blast Programs) to learn about different BLAST programs.