Introduction to wEMBOSS (EMBOSS)

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Introduction to wEMBOSS(EMBOSS)

Maria Wilbe

[email protected]

Department of Animal Breeding and Genetics,

Uppsala, Sweden

Monday, October 26, 2009
mailto:[email protected]:[email protected]


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What is wEMBOSS?

A web interface to the EMBOSS packagefor sequence analysis

Its developed by Martin Sarachu (Argentina)and Marc Colet (Belgium)



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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



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Project files

Create a new file and paste the sequence or upload sequence

Add sequence name to nucList or protList



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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



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Project results Results automatically viewed and saved



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Help within wEMBOSS:

Search

Manual

wossname

Hold mouseover program



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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



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wEMBOSS program: seqret Reads in a sequence and writes it out

Reformat sequences

Get sequences from databases



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Pairvise alignment - Dotup

One sequence is represented on each axis and significantmatching regions are distributed along diagonals in the matrix.



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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.



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Pick primers -eprimer3



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Find microsatellites - equicktandem



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Start working on the tutorial

Login: wemboss1

Password: wemboss1Monday, October 26, 2009

Introduction to wEMBOSS (EMBOSS)

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