Blast+ from NCBI can do multiple blast. It is CLI. The command is very easy to learn. If you want GUI, I think geneious is a good option. It is similar to CLC genomic workbench, but so much cheaper. You can have a free trial here (http://www.geneious.com/).

HI Creg Richard

There is a possiblity to blast multiple sequences against a reference genome ( if it is annotated) using the BLAST+ application. all you need to do is download the latest version of Blast+ application from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. The next step you need to do is download the reference genome from NCBI and make it Blastable database on cmd using the option (-makedlablabledb). the you can easily blast your sequences agaist the reference genome. I hope it helps

Good uck

Blast+ from NCBI can do multiple blast. It is CLI. The command is very easy to learn. If you want GUI, I think geneious is a good option. It is similar to CLC genomic workbench, but so much cheaper. You can have a free trial here (http://www.geneious.com/).

Also, an alternative, you can do it in a terminal and write a loop for that. All you need to do is to download the blat to your linux system or server which you can access.

Geneious from Biomatter has an option called Agent. This is a robot that you can set it to do different task such as those you mentioned.

You can download a free trial this software here:

http://geneious.com/

Also there is a activation patch for its older version (4.8.5).

I can recommend you Blast2GO. Just google it. Good luck.

Or just use blast. You can have a multi-fasta file as the input. If you run from command line use the (m -8) switch to get a nice tabulated output.

/Robert

Long time ago I used bioedit, but now it is quit obsolete…

It is obsolete and some of the links no longer work but BioEdit still works in Win7!

Dear

There is a multialign software named Meg5.2 that you can download it.

I think your problem solve with Mega5 software completely.

adding to Samuels answer:

within blastp+ (from NCBI) you have many options

for how many results you allow maximally ([-max_target_seqs]),

the output format (e.g. [-outfmt 7]) etc.

Why not take all Sequences and blast them against your reference. your output will be one table with all results (clearly separated). That should be most straightforward.

Good luck!

If you use python or biopython with a local blast db then what I have attached will work. It's a bit of code the reads in a fasta file and then queries your local blast db. This will dump everything out into an xml file.

You will need to modify the query options to better fit with what you want and change what data is mined out of the xml file.

I'll post the code that queries the online blast db in a little bit.

EDIT: Way behind on this sorry!!!

BLAST2GO recommended...Much awesome if you run that on a computer cluster

BioPerl (http://www.bioperl.org/wiki/HOWTO:BlastPlus) can also be considered to accomplish this task.

If you are interested to save the output of each input sequence in a separate file, then you can use a scripting language such as Perl.

For example,

open inputfile, "location of your input file";

while()

{

chomp;

#call locally installed blast program using system command

system (http://perldoc.perl.org/functions/system.html);

# in the system command parameters, you can supply the output file name for each input sequence. Moreover, you can parse the top 10 or more hits by storing the output results into a variable.

}

close inputfile;

It is also possible to optimize BioPerl script to store the output results in multiple files.

I hope this helps.

Dear Greg,

Try Blast2Go..automated BLAST and GO annotation...available at http://www.blast2go.com/b2ghome

You can download BLAST locally in your system and run a multi sequence fasta file. You can run the BLAST from command line. This should be able to run one sequence at a time.

Hi Greg,

I wrote a program that automates BLAST for multiple sequences and allows you to visualize and download the results as a table. You are welcome to give it a try:

https://github.com/vforget/blip

This program is geared towards those with little experience in unix or programming.

I look forward to any comments or questions you may have.

In the NCBI website you may find out an answer to this question, I think. Access this url http://www.ncbi.nlm.nih.gov/guide/howto/automate-blast-searches-ncbi-server/ and you'll see how "Automate BLAST searches performed on NCBI servers" using this example http://www.ncbi.nlm.nih.gov/blast/docs/web_blast.pl. I hope to have been helpful.

Wagner's reply has made me think ...

Greg, how many sequences do you have to BLAST? If only a few tens ... maybe a couple hundred, you can submit these using the web interface for NCBI BLAST, where you can limit the number of hits and specify output format.

Thank you all for your responses as they have been a great help!

I wish to BLAST a couple hundred fasta sequences at one time.

This is straight forward with any BLAST application, simply merge all your fasta sequences into one multi-fasta file (using for example the cat command on unix) and uppload this as your BLAST input.

you can ues clustalw program for this work. It is free program.

You can try http://bioinfo.noble.org/plan/ .Hope it works for your project. It is used for the automation of high-throughput BLAST searches

Good suggestion. The PLAN platform automates and includes other resources on the suggestion I did above.

Hi Greg! which program did you use?

Hi Greg! I am a phd student and doing Multiple sequence Blast. Have you got any solutions? Thank you.

https://www.blast2go.com/ Try this Xinxiu 

Hi!! I downloaded the NCBI database to a supercomputer, and in a terminal I did the following command:

blastx -query fastafile -db database -evalue 1E-05 -num_threads 27 -max_target_seqs 1 -max_hsps 1 -outfmt 6 > out_file

Thank you guys for Blast2Go suggestion. 

How to run a local Blast against a custom database:

https://www.youtube.com/watch?v=ujCEp9ZwcJw

Blast2GO allows you to create your own Blast database from a single or multi-species FASTA file using the option "Make Blast Database". Once the database is formatted it can be used to run a local Blast.