SIB Bioinformatics Workshops

Introduction to wEMBOSS

Friday May 11, 2007

Quizz

Question 1
Do you need to authenticate to use wEMBOSS ?
Yes, always No, it is not required
Question 2
Once you are logged in, what do you need to do first?
start to work on your project select an existing project in the project management window or create a new project read and accept the legal terms upload your project to the server
Question 3
You want to extract a DNA sequence in FASTA format from the EMBL database, how do you proceed?
Use the fetch program and copy&paste the result into the seqret window Search for the available databases with showdb, then use seqret to retrieve the sequence Create a new file within the project, edit the file to insert the sequence Go to the EBI and drag&drop the file into your project directory Upload the file from your local computer to your project directory
Question 4
You are looking for a program to translate a DNA sequence into a protein sequence
ask an experienced colleague search with Google with "EMBOSS translate DNA to protein" use the keyword search tool with "translate" browse the program menu under "Nucleic -> Translation"
Question 5
How do you extract the coding region (CDS) of a mRNA?
get the mRNA sequence by email and copy&paste the sequence to your project use the program extractfeat with "type=CDS" option use the program coderet use the program extractseq with manually selected exons
Question 6
You want to create a random database of protein sequences, how do you proceed?
use the program makeprotseq use the program shuffleseq on a subset of Swiss-Prot use your keyboard to generate the sequences by random typing use the program msbar on a subset of Swiss-Prot
Question 7
You have a mouse EST sequence that you want to align to a cat genomic sequence, which program(s) could you choose?
esim4 (EMBASSY) with default parameters est2genome with default parameters needle with default parameters stretcher with default parameters
Question 8
How do you create a multiple sequence alignment with all sequences matching UBP*_RAT in Swiss-Prot ?
Use water to align each pair and join the pairs into a multiple alignment Use emma (clustalw) directly Do a Blast on ExPASy with UBP7_RAT and collect the RAT matches Use seqret to retrieve all sequences individually and store them in a file, then use emma (clustalw)