Question: In Silico Genome Digestion ?
6
gravatar for Bioch'Ti
10.2 years ago by
Bioch'Ti1.0k
France (Avignon)
Bioch'Ti1.0k wrote:

Hi Guys,

I would like to find a tool that simulates the 'in silico' digestion of an eukaryote genome (not fully sequenced but EST/454 available) by the most frequently used restriction enzymes. My goal is to know, how many fragments and repetitive elements are generated, what are their average sizes, etc... depending of the enzyme. This will help me to know which enzyme is the best one to prepare gDNA libraries for NGS.

Cheers.

ADD COMMENTlink modified 9.5 years ago by Jason0 • written 10.2 years ago by Bioch'Ti1.0k

Thanks for the clarification on the sequencing status of the organism!

ADD REPLYlink written 10.2 years ago by Daniel Swan13k

I also want to know how to save the output in a file, would you mind adding a few lines. Thanks!

ADD REPLYlink written 9.7 years ago by Jason0
8
gravatar for Pierre Lindenbaum
10.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

Brute force: the following java program prints all the restriction sites (type II) (chromosome, start, end, size) for all the chromosomes of the human chromosomes. Hope it helps:

Compilation:

javac Digest.java

Execution:

java Digest

Output:

chr1    AatII    0    47476    47476
chr1    AatII    47476    70600    23124
chr1    AatII    70600    164453    93853
chr1    AatII    164453    170555    6102
chr1    AatII    170555    175979    5424
chr1    AatII    175979    325093    149114
chr1    AatII    325093    360629    35536
chr1    AatII    360629    369596    8967
chr1    AatII    369596    568607    199011
chr1    AatII    568607    568665    58
chr1    AatII    568665    620090    51425
(...)
ADD COMMENTlink modified 22 months ago by RamRS27k • written 10.2 years ago by Pierre Lindenbaum129k
1

This java program provided all the results I needed with less hassle than many of the web-based tools I had tried. Thanks!

ADD REPLYlink written 9.7 years ago by Mrawlins420

As you said, Brute Force! Thnaks very much for you detailed and helpful answer!

ADD REPLYlink written 10.2 years ago by Bioch'Ti1.0k

0

If I want to give a sequential number to each fragment and also the sequence itself in the output file, can you modify the java program for that purpose. Thanks

an

ADD REPLYlink written 9.7 years ago by Jason0

The program is great! I also want to know how to save the result into a output file. Thanks

ADD REPLYlink written 9.7 years ago by Jason0

This java script for in silico restriction digestion does not do reverse complementary search, am I right ?

ADD REPLYlink written 3.0 years ago by szhou0

This java script for in silico restriction digestion does not do reverse complementary search, am I right ?

https://en.wikipedia.org/wiki/Palindromic_sequence#Restriction_enzyme_sites

ADD REPLYlink written 3.0 years ago by Pierre Lindenbaum129k
5
gravatar for Louis Letourneau
10.2 years ago by
Montreal
Louis Letourneau800 wrote:

EMBOSS has an app that does this from REBASE database: http://emboss.open-bio.org/wiki/Appdoc:Restrict

In fact, EMBOSS has many tools to play with REBASE or restriction enzymes in nucleotide or amino acid spaces.

ADD COMMENTlink modified 22 months ago by RamRS27k • written 10.2 years ago by Louis Letourneau800
2

If you have Eukariotic sized genome (say 100Mb+) you will have to install EMBOSS on a local computer and use command line. On Ubuntu and Debian you can install it by typing: sudo apt-get install emboss

Check also http://packages.ubuntu.com/karmic/science/emboss

ADD REPLYlink written 10.2 years ago by Darked894.2k
1

I just tried this Emboss package, but there are two limitations: the amount of sequences that you can upload (it has crashed with a 5Mb fasta file) and it didn't give me the length of the generated fragments by the list of the enzymes... However, it worked.

ADD REPLYlink written 10.2 years ago by Bioch'Ti1.0k
3
gravatar for Daniel Swan
10.2 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

From an already sequenced organism?

You might want to look at : http://insilico.ehu.es/digest/ (ok that's prokaryotes!)

For eukaryotes: http://insilico.ehu.es/eukaryota/digest/

They also have a tool for long DNA sequence length digests here: http://insilico.ehu.es/restriction/long_seq/

ADD COMMENTlink modified 10.2 years ago • written 10.2 years ago by Daniel Swan13k

Oops, posted too fast, that's not for eukaryotic genomes..

ADD REPLYlink written 10.2 years ago by Daniel Swan13k
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