Exercise 1

Exercise 1 : Fundamentals of Sequence Analysis

A) Sequence formats and conversion

Go to

https://www.ebi.ac.uk/Tools/sfc/

Upload the sequence or paste in the query  window. Select a genBank or fasta out put format. You may also try  other format conversions.

B) Translating sequences
Use the 

https://www.ebi.ac.uk/Tools/st/emboss_transeq/

to produce formatted output

C) Viewers for sequence data Magic sequence viewer

D) Finding open reading frames

Sequence Modification suite is used to analyse various parameters of DNA and protein sequences

http://bioinformatics.org/sms/

Go to www.expasy.ch

1. Under proteomics tools, choose DNA->protein

2. Choose Translate (note the other sites with similar functions)

3. Copy the BTU89872 sequence from WordPad (FASTA format), and paste it into the sequence box on the Translate web page

4. Translate the sequence

5. Return to Expasy, this time choose Translation Machine at EBI

6. Paste the sequence into the sequence box

7. Try the different options for reading frames and start/stop positions

Use the  Emboss tool "transeq" to translate the L01655 sequence. Try different code tables. Use "tfm transeq" to view the manual page

Use the Emboss modules "getorf" and "plotorf" to analyze the sequence

E) Determining protein and DNA characteristics

1. Obtain the nucleic acid sequence L01654.

2. Obtain the protein sequence for BAB83506.

3. Analyze them with the following tools:

BCM Search Launcher

SMART

Pfam

Prosite

Prints

If you have some time left, redo some of the exercises with sequences that are of interest to yourself

BTU89872

AF039908