Download presentation
Presentation is loading. Please wait.
Published byDwayne Preston Modified over 9 years ago
1
Copyright OpenHelix. No use or reproduction without express written consent1
2
Melina II A Web-Based Tool for Promoter Analysis Materials prepared by: Sawsan Khuri, Ph.D. www.openhelix.com Version 3.0
3
Copyright OpenHelix. No use or reproduction without express written consent3 Melina II Agenda Introduction and Credits Basic Searches Explanation of Algorithms CONSENSUS MEME Gibbs Motif Sampler MDscan Understanding the Results Summary Exercises Melina II: http://melina2.hgc.jp
4
Copyright OpenHelix. No use or reproduction without express written consent4 Introduction and Credits
5
Copyright OpenHelix. No use or reproduction without express written consent5 Melina II Credits algorithms references
6
Copyright OpenHelix. No use or reproduction without express written consent6 Melina II - Finding Help
7
Copyright OpenHelix. No use or reproduction without express written consent7 Melina II Agenda Introduction and Credits Basic Searches Summary of Algorithms CONSENSUS MEME Gibbs Motif Sampler MDscan Understanding the Results Summary Exercises Melina II: http://melina2.hgc.jp
8
Melina II - Where to Start Copyright OpenHelix. No use or reproduction without express written consent8 FASTA FORMAT: >GENE_1_ID and a few words accgtgggatggacgctgagctgaccaaagct agatcgaatatagactagcatgatcggataga >GENE_2_ID and a few words atatagcagtcgggatggacgctgagctgata gatcgatgctagtcgatagctgatgcta >GENE_3_ID and a few words atcgatggtgctgataacacgatgctgacgat gctagatcgatcgagcatgggatggacgctga gctgacatccgact ¶ ¶
9
Copyright OpenHelix. No use or reproduction without express written consent9 Melina II - Basic Searches
10
Copyright OpenHelix. No use or reproduction without express written consent10 Input Example
11
Copyright OpenHelix. No use or reproduction without express written consent11 Job Running Job ID
12
Sneak Preview of Results Copyright OpenHelix. No use or reproduction without express written consent12
13
Copyright OpenHelix. No use or reproduction without express written consent13 Melina II Agenda Introduction and Credits Basic Searches Explaining the Algorithms CONSENSUS MEME Gibbs Motif Sampler MDscan Understanding the Results Summary Exercises Melina II: http://melina2.hgc.jp
14
Copyright OpenHelix. No use or reproduction without express written consent14 Explaining the Algorithms - Consensus CONSENSUS: http://bifrost.wustl.edu/consensus/index.html
15
Copyright OpenHelix. No use or reproduction without express written consent15 Melina II - Consensus Parameters scroll
16
Copyright OpenHelix. No use or reproduction without express written consent16 Explaining the Algorithms - MEME MEME: http://meme.sdsc.edu/meme/intro.html
17
Copyright OpenHelix. No use or reproduction without express written consent17 Melina II - MEME Parameters
18
Copyright OpenHelix. No use or reproduction without express written consent18 Explaining the Algorithms - Gibbs Gibbs Motif Sampler: http://bayesweb.wadsworth.org/gibbs/gibbs.html
19
Melina II - Gibbs Parameters 19
20
Copyright OpenHelix. No use or reproduction without express written consent20 Explaining the Algorithms - MDscan MDscan: http://ai.stanford.edu/~xsliu/MDscan/
21
Melina II - MDscan Parameters 21
22
Copyright OpenHelix. No use or reproduction without express written consent22 Choosing the Method
23
Explaining the Algorithms - More Information CONSENSUS: http://bifrost.wustl.edu/consensus/index.html MEME: http://meme.sdsc.edu/meme/intro.html Gibbs Motif Sampler: http://bayesweb.wadsworth.org/gibbs/gibbs.html MDscan: http://ai.stanford.edu/~xsliu/MDscan/ 23
24
Copyright OpenHelix. No use or reproduction without express written consent24 Melina II Agenda Introduction and Credits Basic Searches Explaining the Algorithms CONSENSUS MEME Gibbs Motif Sampler MDscan Understanding the Results Summary Exercises Melina II: http://melina2.hgc.jp
25
Copyright OpenHelix. No use or reproduction without express written consent25 Understanding the Results - Left Hand Panel
26
Copyright OpenHelix. No use or reproduction without express written consent26 Understanding the Results - Summary View
27
Copyright OpenHelix. No use or reproduction without express written consent27 Understanding the Results - Navigation Tools
28
Copyright OpenHelix. No use or reproduction without express written consent28 Understanding the Results - the Zoom Tool
29
Copyright OpenHelix. No use or reproduction without express written consent29 Understanding the Results - the Fit Tool
30
Copyright OpenHelix. No use or reproduction without express written consent30 Understanding the Results - Lower Panel
31
Copyright OpenHelix. No use or reproduction without express written consent31 Understanding the Results - CONSENSUS clicked
32
Copyright OpenHelix. No use or reproduction without express written consent32 Understanding the Results - Gibbs Sequence Alignment Logo Diagram Further analysis clicked
33
Copyright OpenHelix. No use or reproduction without express written consent33 Understanding the Results - MDscan clicked Sequence Alignment Logo Diagram Further analysis
34
Copyright OpenHelix. No use or reproduction without express written consent34 Understanding the Results - MEME clicked
35
Copyright OpenHelix. No use or reproduction without express written consent35 Understanding the Results - Further Analysis
36
Copyright OpenHelix. No use or reproduction without express written consent36 Melina II Agenda Introduction and Credits Basic Searches Explaining the Algorithms CONSENSUS MEME Gibbs Motif Sampler MDscan Understanding the Results Summary Exercises Melina II: http://melina2.hgc.jp
37
Copyright OpenHelix. No use or reproduction without express written consent37 Sequence Alignment Logo Diagram Further analysis Motifs Choose parameters Results Input sequences Summary
38
Copyright OpenHelix. No use or reproduction without express written consent38 Melina II Agenda Introduction and Credits Basic Searches Explaining the Algorithms CONSENSUS MEME Gibbs Motif Sampler MDscan Understanding the Results Summary Exercises Melina II: http://melina2.hgc.jp
39
Copyright OpenHelix. No use or reproduction without express written consent39
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.