Author Archives: Andrea Telatin

Apr 16 2012
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lesson

Tursday lessons

Dear all, the Dept. organized a workshop on RNA world. You’ll attend the seminars as part of the course.

RNA world: a never ending story

Speakers:

  • Katia Basso (Institute for Cancer Genetics, Columbia University, NY, USA)
  • Paola Guglielmelli (Dept. of Hematology, University of Florence, Italy)
  • Sergio Marchini (“Mario Negri” Institute for Pharmacological Research, Dept. of Oncology, Milan, Italy)
  • Irene Bozzoni (Dept. of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Italy)
  • Daniela Taverna (Molecular Biotechnology Center, University of Turin, Italy)

Further info here.

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Apr 13 2012
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lesson

Choose your next lesson!

On Monday we’ll have 2 hours lesson together (standard GV time)… Help us realizing a useful lesson!

prepare to tell us about you curiosities and questions concerning what we have done during the practicals or what we’re going to do next, concerning perl and concerning what you can do with genomics and bioinformatics.. and what you would do if you were a researcher !

Apr 06 2012
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perl

Take a self-test

If you want to test your Perl skills try this online test made for you 🙂

Let me know your score!

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Mar 30 2012
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perl

Good work guys! (final script solution)

Again, you outperformed! We still have to check your primers but you worked as scientist should, with care and analyzing alternative hypotesis rather than launching a couple of programs and taking note of the output. Good work!

Some of you asked for the script. Well, you deserve something more: an updated script 🙂
Did you notice the bottleneck of the script? It takes a while to load the sequence of the two contigs parsing a long file. So I decided to split the 454contigs.fna file producing 1 file for each contig. Thus knowing the name of the contig, you can directly open its file (eg. contig00323.fna).

The script (after the breack) was accordingly modified…

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Mar 30 2012
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laboratory, perl

Fifth lab: pick your primers

Today we’ll meet at 1.30 pm in aula F pr to finish together our “pick-primers.pl” program. During last lab most of you got Primer3 running with our custom parameters. Primer3 output consists in a list of possible primer pairs.

We want to blast each primer against reference contigs to check how many sequence similar to it are present in the genome. This is a pivotal test to have specific PCRs. To make this we design a subroutine called ‘blast’ that takes as input a sequence (primer) and blast it against the contigs and parses the output returning a list of hints. In particular we consider dangerous those aligment long as the query -2 bp. Thus if our primers is long 20 and the match is 15 we will discard it. If the match with another contig is 18 bases long, we will report this to the user.

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Mar 28 2012
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messages

Just to know…

Last class lessons were on physical mapping approaches, from radiation hybrids to Happy Mapping and BEP-Mapping with NGS. These are quite interesting topics and we would like to know if you understood them.

Please answer the poll below!

Happy mapping and BEP-mapping: did you understand these techniques?

View Results

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Mar 27 2012
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homeworks

An (optional) exercise to test your skills

Look at our pick-primers.pl script: I added some ASCII characters to draw a box around the welcome screen. Now it looks like:

print STDERR "
 +----------------------------------------------+
 |   Pick Primer Tool v.01                      |
 |                                              | 
 |   Parameters:                                |
 |   contig1 direction1 contig2 direction2      |
 |                                              |
 |   direction1,2 = U or C                      |
 +----------------------------------------------+
";

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Mar 26 2012
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laboratory, perl

Lab 4: solution

Click “read more” to see today’s solution…

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Mar 26 2012
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laboratory, perl

Fourth lab: shell commands via Perl

Today we:

  • have a small lesson on shell commands with Perl
  • optimize last time’s script so that Primer3 execution will be faster in most cases
  • see some more example of regular expressions
Mar 25 2012
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perl

Small project on genome shotgun: comparing results

As some of you correctly understood the script with no name and no instructions takes as input a single sequence and simulate a whole genome shotgun.

It takes three parameters: filename of the sequence, desired coverage and read length.

I used Yeast chromosome 2 as sequence for tests, and tried both with 20X and 50X coverage with increasing read length from 50bp (SOLiD like) to 400bp (454 like) and 800bp (Sanger like).

All the datasets were independently assembled with Newbler. We know that we started from a single sequence  573,563 bp long.

"de novo" assembly with Newbler: results

 

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