26 May 07 - 00:46RNA Folding Slides

Lesson 25/05/2007

RNA Folding

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17 July 06 - 20:27PDB for the exams 18 July 2006

• DNA Structure A DNA
• DNA Structure B DNA
• DNA Structure Z DNA

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18 June 06 - 00:09Date for exams

• 28 June 2006 - 10:00 am  Room I - Mathemathics Building
  (Book the exam, -writing me an email with your name and surname- at least a week before)
  
• 18 July 2006 - 10:00 am  Room I - Mathemathics Building
  (Book the exam, -writing me an email with your name and surname- at least a week before)

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18 June 06 - 00:00Practice 12 and 14 06 2006

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15 June 06 - 10:42Slides 15 06 2006

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15 June 06 - 10:24Rasmol

  
• Download Rasmol
• Download Help
• DNA A Structure
• DNA B Structure
• DNA Z Structure
• ATP Structure
• Hemoglobin
• Trypsin BTI
• tRNA

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07 June 06 - 17:40Next lessons

Laurea Specialistica in Biologia Molecolare

On Monday 12 June 2006 - 10:00-13:00  Aula LA2
On Thursday 15 June 2006 - 10:00-13:00  Aula I

Laurea Triennale in Biotecnologie

On Wednesday 14 June 2006 - 15:00-17:00  Aula LA2
On Thursday 15 June 2006 - 10:00-13:00  Aula I

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07 June 06 - 17:35Slides 11/05/2006

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11 May 06 - 16:07Very useful plugins for FireFox

• BioBar - aims at implementing various bioinformatics tools as an extension on the Mozilla based browsers.
• BioFox - The biobar project is a bioinformatics power-browsing toolbar for Mozilla-based browsers including Firefox and Netscape 7+. This toolbar provides access to all major biological data resources. The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases. In addition to the browsing features, biobar also provides links to important bioinformatics sites and services including services at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ). The tool also provides links to major data deposition sites for nucleotide, protein and 3D-structure data. Finally, the menu also contains links to many Sequence, Structure alignment and analysis tools. The latest release (Version 1.4) of biobar provides browsing access to over 46 different databases (including Google Scholar, HubMed, SCIRUS etc) (listed here). If you have downloaded,used and liked biobar, please spread the word by adding this icon to your webpage using the code below.

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11 May 06 - 15:58Sequence alignment tools

Local Alignment

• Blast nucleotide
• Blast protein
• Translated Blast
• FastA by Virgina Edu
• FastA by EBI

Global Alignment

• ClustalW

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11 May 06 - 15:40Notes 4/05/2006

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06 May 06 - 00:13Introduction to Biological Databases and Sequence Manipulation - Try and learn

An exercise proposed by Molecular Lab
Getting started: text queries in databases
File formats, text queries, simple sequence manipulation on the web.

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04 May 06 - 15:03Changing room again !!!!

Next lecture will be held at Mathematics department Aula I.

Please sign up for the authorization to use computers in Aula I at Department of mathematics as soon as possible. To do this, you have to request a form to be filled at janitor's lodge portineria in italian (ask to Pino) at Department of mathematics.

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04 May 06 - 10:03Slides 27/04/2006

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04 May 06 - 09:45Secondary Databases

• Uniprot
• RefSeq
• Swiss-Prot (ExPASy)
• Protein Data Bank

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04 May 06 - 09:35Primary Databases

• DNA DataBase of Japan
• EMBL Nucleotide Sequence database
• GenBank

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03 May 06 - 18:48DNA Sequence utilities

Dowload an EMBL DNA test Sequence

Dowload a FASTA DNA test Sequence

• Convert a sequence (with readseq): change DNA/protein sequence to almost any format
• Shuffle a sequence: randomize a DNA/protein sequence to use as a statistical control
• Clean a sequence: remove numbers, spaces, and other non-sequence characters
• Reverse Complement
• ORF finder from NCBI
• Six frame translation
• Restriction Enzyme Map Analysis: Generate a map of enzyme sites
• Graphical Restriction Map:Create a graphical Restriction Map
• NEBcutter:Another tool for graphical Restriction Map
• Manipulate and Display a DNA sequence

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25 April 06 - 01:47Getting the authorization to use computers in LA2

Please sign up for the authorization to use computers in LA2 at "Polo d'Informatica" building as soon as possible. To do this, you have to request a form to be filled at janitor's lodge portineria in italian (ask to Beatrice) of "Polo d'Informatica" building.

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25 April 06 - 00:36Recommended Course Textbook

	Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd Edition Andreas D. Baxevanis (Editor), B. F. Francis Ouellette (Editor), Wiley
	Introduzione alla Bioinformatica, Valle G., Helmer Citterich M., Attimonelli M., Pesole G., Zanichelli

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25 April 06 - 00:06General Course Information

Lectures - Thursdays 10:00am-13:00am
Place - Room LA2 (Polo d’Informatica)
Period - 19 April 2006 - 16 June 2006

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