introduction to wemboss (emboss)
TRANSCRIPT
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
1/18
Introduction to wEMBOSS(EMBOSS)
Maria Wilbe
Department of Animal Breeding and Genetics,
Uppsala, Sweden
Monday, October 26, 2009
mailto:[email protected]:[email protected] -
8/14/2019 Introduction to wEMBOSS (EMBOSS)
2/18
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
3/18
What is wEMBOSS?
A web interface to the EMBOSS packagefor sequence analysis
Its developed by Martin Sarachu (Argentina)and Marc Colet (Belgium)
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
4/18
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
5/18
Create a project wEMBOSS uses the concept of projects
nucList & protList are automatically created (addnames of the sequences you wish to access)
Select project
Create new files, view,edit, remove
Create new projectsand subprojects
Upload files
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
6/18
Project files
Create a new file and paste the sequence or upload sequence
Add sequence name to nucList or protList
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
7/18
Selection of programs/files
Drop-down menu withall available programs
Select a program byclicking on its name.
Choose a sequence towork with from:
- list selector: to select asequence from nucList orprotList
- local computer file: to
upload a file from yourcomputer
- EMBOSS database: toaccess a sequence from aserver
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
8/18
Project results Results automatically viewed and saved
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
9/18
Help within wEMBOSS:
Search
Manual
wossname
Hold mouseover program
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
10/18
wEMBOSS program: wossname
Easy to forget a program name
To find programs, use wossname
wossname finds programs by looking for keywords in thedescription or the name of the program
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
11/18
wEMBOSS program: seqret Reads in a sequence and writes it out
Reformat sequences
Get sequences from databases
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
12/18
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
13/18
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
14/18
Pairvise alignment - Dotup
One sequence is represented on each axis and significantmatching regions are distributed along diagonals in the matrix.
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
15/18
Multiple alignment -prettyplot
Identical residues are shown in red, and similar residues ingreen
This type of display can give you a first impression of regions ofconservation.
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
16/18
Pick primers -eprimer3
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
17/18
Find microsatellites - equicktandem
Monday, October 26, 2009
-
8/14/2019 Introduction to wEMBOSS (EMBOSS)
18/18
Start working on the tutorial
Login: wemboss1
Password: wemboss1Monday, October 26, 2009