Download - Visualise conservation
Slide 1
Visualise conservationEMBO Workshop, Cape Town, 2014Colour -> BLOSUM621.
1Reduce redundancyEdit-> Remove Redundancy1.PICK 80%2.
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3Edit-> Remove Empty Columns1.EMBO Workshop, Cape Town, 2014
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EMBO Workshop, Cape Town, 2014Define boundaries5Define boundariesColour -> Hydrophobicity1.
EMBO Workshop, Cape Town, 20146
TUM, January 20132KX7 model 1
EEVTESER7
CLICK on residue number bar to select column1.Edit -> Remove right2.EMBO Workshop, Cape Town, 2014Trim alignment8
EMBO Workshop, Cape Town, 2014Trim alignmentCLICK on residue number bar to select column1.Edit -> Remove left2.9
Save SEED alignmentFile -> Save as RcsD-ABL-SEED-ali.fasta 1.EMBO Workshop, Cape Town, 201410
Create HMM and run against database(s)EMBO Workshop, Cape Town, 2014CLICK on Start1.11
Create HMM and run against database(s)EMBO Workshop, Cape Town, 2014CLICK on Choose File1.Choose RcsD-ABL-SEED-ali.fasta 2.12
First run against RP75 to see if anything has changedEMBO Workshop, Cape Town, 2014CLICK on rp751.13First run against RP75 to see if anything has changed
BEFORE
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Now we run against UniProtKBEMBO Workshop, Cape Town, 201417Check ScoresEMBO Workshop, Cape Town, 2014
18Check Low ScoresEMBO Workshop, Cape Town, 2014
19Define significance thresholdEMBO Workshop, Cape Town, 2014
20Check taxonomic distributionEMBO Workshop, Cape Town, 2014
21Check taxonomic distributionEMBO Workshop, Cape Town, 2014
22Check architectures
23Save HMMEMBO Workshop, Cape Town, 2014
24EMBO Workshop, Cape Town, 2014Job done?25
TUM, January 2013
2KX7Pick a target regionEMBO Workshop, Cape Town, 2014Schme et al. Structure 2011 26
TUM, January 2013
2KX7Pick a target regionEMBO Workshop, Cape Town, 2014RcsD_ABL (PF16359)Schme et al. Structure 2011 27
TUM, January 2013
2KX7Pick a target regionEMBO Workshop, Cape Town, 2014RcsD_ABL (PF16359)Schme et al. Structure 2011 28EMBO Workshop, Cape Town, 2014
Schme et al. Structure 2011 2KX7Job done?2AYY29EMBO Workshop, Cape Town, 2014Job done?
30EMBO Workshop, Cape Town, 2014ExerciseRun the UNIPROT ID: Q820A8with the hmmer website (2 iterations) and observe results31EMBO Workshop, Cape Town, 2014ExerciseRun the UNIPROT ID: Q820A8with the hmmer website (2 iterations) and observe results
Run the Q820A8-PASTA-domain.fastawith the hmmer website (2 iterations) and observe results32EMBO Workshop, Cape Town, 2014ExerciseRun the UNIPROT ID: Q820A8with the hmmer website (2 iterations) and observe results
Run the this portion of the Q820A8 sequenceVTLSDYSGISYDNAVSRLIALGIPESQIKRVDEESDKVEKDTVISQEPASGTAVDPKNDTITLHVSKwith the hmmer website (2 iterations) and observe results33EMBO Workshop, Cape Town, 2014AcknowledgementsRob Finn (Protein Family Team Leader)
The Pfam Team:Penny CoggillRuth EberhardtJaina MistryJohn TateIlias Lavidas
Alex Bateman (Protein sequence resources cluster)Sean Eddy -> HMMER3 (Janelia Farm)Erik Sonnhammer (Stockholm University)
All organisers of the EMBO course, trainers and trainees
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