Melting 5 - How to run in batch mode

[Nicolas Rodriguez]

Forwarding this post from the old sourceforge forum as it could be useful to some users.

Hi Nicolas,

Thank you for your answer. It made the trick !

I thought it would much more complicated to handle a large set of sequences.

Thanks a lot,

I will come back to you if I need more technical information,

Regards,

Laurent

-----Message d'origine-----

De : Nicolas Rodriguez [mailto:rodri...@babraham.ac.uk] 

Envoyé : jeudi 18 juin 2015 12:30

À : DRAZEK Laurent

Cc : nicolas lenovere; gen...@discussion.melting.p.re.sf.net

Objet : RE: Melting 5 - How to run in batch mode

Hi Laurent,

> -------- Forwarded Message --------

> Subject: RE: Melting 5

> Date: Thu, 18 Jun 2015 11:26:48 +0200

> From: DRAZEK Laurent <Laurent...@biomerieux.com>

> To: n.len...@gmail.com <n.len...@gmail.com>

>

> Bonjour,

>

> Je reviens vers vous, suite à notre précédent échange.

> Comme je vous l'indiquais, nous aimerions nous appuyer sur MELTING5 

> pour calculer des delta_G0 pour des hybrides ADN/ADN.

> Nous avons un très grand nombre de valeurs à compiler et votre package 

> semble avoir un mode "batch" qui nous serait bien utile.

>

> Je n'ai trouvé aucune documentation associée à ce mode "batch", en 

> particulier comment formater le fichier d'entrée contenant les séquences.

>

> Pourriez-vous m'aider ?

>

So your question is how to use melting to calculate melting temperatures for a large number of sequences.

For this you can use the 'melting-batch' script or directly the 'melting.BatchMain' java class.

The format of the command is: 'melting-batch [OPTIONS] sequencefile'

Here [OPTIONS] mean all of you standard melting options, excluding the -S or -C. Then a sequencefile, this has to be the last argument.

How to format the sequence file? You need to put one sequence per line, for each non empty line in the file a melting temperature will be calculated.

You have the option to also put the complementary sequence, on the same line, separated by a space or tab.

Let us know if it work for you,

Thanks,

Nico

[Piero Dalle Pezze]

So would the following be a suitable sequence input file for Melting?

<--- file starts here --->

GCAGCAGC

GCAGCAGCAGC

GCAGCAGCAGCAGC

GCCGCCGC

GCCGCCGCCGC

GCCGCCGCCGCCGC

GCGGCGGC

GCGGCGGCGGC

GCGGCGGCGGCGGC

GCUGCUGC

GCUGCUGCUGC

GCUGCUGCUGCUGC                                                                     

GCAGCAGCAGCAGCAGC

GCAGCAGCAGCAGCAGCAGC

GCAGCAGCAGCAGCAGCAGCAGC

GCGGCGGCGGCGGCGGC

GCGGCGGCGGCGGCGGCGGC

GCGGCGGCGGCGGCGGCGGCGGC

GCUGCUGCUGCUGCUGC

GCUGCUGCUGCUGCUGCUGC

GCUGCUGCUGCUGCUGCUGCUGC

GCCGCCGCCGCCGCCGC

GCCGCCGCCGCCGCCGCCGC

GCCGCCGCCGCCGCCGCCGCCGC

<--- file ends here --->

                     

--
You received this message because you are subscribed to the Google Groups "melting-forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to melting-foru...@googlegroups.com.
To post to this group, send email to meltin...@googlegroups.com.
To view this discussion on the web, visit https://groups.google.com/d/msgid/melting-forum/8db37e7e-271b-483c-a516-ee6a2ddcfe53%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Nicolas Rodriguez]

Yes, one sequence per line, as said in the previous post.

Nico

-----Message d'origine-----

De : Nicolas Rodriguez [mailto:rodriguezn@babraham.ac.uk] 

To unsubscribe from this group and stop receiving emails from it, send an email to melting-forum+unsubscribe@googlegroups.com.

[Piero Dalle Pezze]

Okay, so the file src/examples/test/CNGSequences.txt (same data) is a result file? 

-----Message d'origine-----

De : Nicolas Rodriguez [mailto:rodri...@babraham.ac.uk] 

To unsubscribe from this group and stop receiving emails from it, send an email to melting-foru...@googlegroups.com.

To post to this group, send email to meltin...@googlegroups.com.
To view this discussion on the web, visit https://groups.google.com/d/msgid/melting-forum/8db37e7e-271b-483c-a516-ee6a2ddcfe53%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "melting-forum" group.

To unsubscribe from this group and stop receiving emails from it, send an email to melting-foru...@googlegroups.com.

To post to this group, send email to meltin...@googlegroups.com.

To view this discussion on the web, visit https://groups.google.com/d/msgid/melting-forum/794630a5-466e-44e0-b8bf-a8ee288588aa%40googlegroups.com.

[Piero Dalle Pezze]

Okay, so this is a validation file where the expected melting temperature for each sequence is provided: 

(file src/examples/test/CNGSequences.txt)

# Broda et al (2005). Biochemistry 44: 10873-10882.

# 0.0001 M oligomer concentration.1 M sodium chloride, 20 mM sodium cacodylate, and 0.5 mM Na2EDTA, pH 7.

GCAGCAGC=39.8 

GCAGCAGCAGC=48.1 

GCAGCAGCAGCAGC=51.4                                      

GCCGCCGC=41.6 

GCCGCCGCCGC=44.9 

GCCGCCGCCGCCGC=46.0

GCGGCGGC=44.2 

GCGGCGGCGGC=59.5 

GCGGCGGCGGCGGC=65.6

GCUGCUGC=33.7 

GCUGCUGCUGC=44.3 

GCUGCUGCUGCUGC=52.2                                                                              

GCAGCAGCAGCAGCAGC=65.2

GCAGCAGCAGCAGCAGCAGC=68.0

GCAGCAGCAGCAGCAGCAGCAGC=68.8

GCGGCGGCGGCGGCGGC=69.0

GCGGCGGCGGCGGCGGCGGC=69.0

GCGGCGGCGGCGGCGGCGGCGGC=74.2

GCUGCUGCUGCUGCUGC=60.6

GCUGCUGCUGCUGCUGCUGC=62.9

GCUGCUGCUGCUGCUGCUGCUGC=65.2

GCCGCCGCCGCCGCCGC=65.0

GCCGCCGCCGCCGCCGCCGC=65.6

GCCGCCGCCGCCGCCGCCGCCGC=67.2 

[t.be...@agruni.edu.ge]

Hi Nicolas,

How long molecules can be analyzed - 160 kb?