How do I install Blast2go 3 on Ubuntu


Blast2go is an indispensable Bioinformatic software tool for the automated, high-throughput functional annotation of novel sequence. Since it si a java based programme therefore you can easily install Blast2go to any machine, windows, linux, mac. Very recently authors of Blast2go released the new version of  Blast2go that will be known as Blast2go 3. New version of Blast2go has nice colorful user interface. Unlike the older version Blast2go 2.8 which can run by java webstart, you have to install the Blast2go 3 on your machine.

Installation steps (for 64 bits Ubuntu machine)

  • Download  Blast2go 3 installation file from HERE
  • Extract the .zip file
  • Run the Blast2GO_unix_3_0_x64.sh file through terminal and follow the instructions
  • Now you are set to run the brand new Blast2GO 3
How do I install Blast2go on Ubuntu HERE

How to Predict ORF from Multiple Fasta Sequence

Previously I shared the Bioinformatics tools for DNA or RNA manipulation and multiple DNA sequence translator. Although withmultiple DNA sequence translator we can convert several DNA to protein but I got stuck when I decide to predict open reading frame (ORF) out of several expression sequence tags (EST). Although in theory, both DNA to protein translator and ORF predictor do similar kind of task but there are some basic difference in both result. Although I tried several tools to predict ORF out of several hundred ESTs but, in my opinion, ORF predictor by Dr. X. Min was the best.
I tested this Bioinformatics tools for ORF prediction multiple fasta sequence and all the time it was 100% accurate. You can use ORF predictor as server from HERE or you can write to Dr. Min to use the ORF predictor as a offline tools. It contains 2 wonderful simple PERL script that work efficiently and accurately.
How to Remove Duplicate Sequences from a multi fasta Files HERE

How Do I Install CD-HIT on Ubuntu

CD-HIT is a popular bioinformatics software for clustering and comparing protein or nucleotide sequences. Although I downloaded the CD-HIT and followed the instruction in CD-HIT manual but it doesn't work for me. Then I decided to download CD-HIT directly from Ubuntu software center. Only a single command worked like a charm for me<
sudo apt-get install cd-hit

Remember when I tried to run this command apt-get install cd-hit I got an error like this
E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied)
E: Unable to lock the administration directory (/var/lib/dpkg/), are you root?
So just avoid the mistake I did. So after running this command I got this success message
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  linux-headers-3.13.0-32 linux-headers-3.13.0-32-generic
  linux-image-3.13.0-32-generic linux-image-extra-3.13.0-32-generic
Use 'apt-get autoremove' to remove them.
The following NEW packages will be installed:
  cd-hit
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 701 kB of archives.
After this operation, 1,316 kB of additional disk space will be used.
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty/universe cd-hit amd64 4.6.1-2012-08-27-2 [701 kB]
Fetched 701 kB in 1s (507 kB/s) 
Selecting previously unselected package cd-hit.
(Reading database ... 306437 files and directories currently installed.)
Preparing to unpack .../cd-hit_4.6.1-2012-08-27-2_amd64.deb ...
Unpacking cd-hit (4.6.1-2012-08-27-2) ...
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Processing triggers for doc-base (0.10.5) ...
Processing 1 added doc-base file...
Setting up cd-hit (4.6.1-2012-08-27-2) ...

I got this option when I run the cd-hit-est from my root

how do i install Blast2go on Ubuntu