Applications Using standard Bioinformatics applications.
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Transcript of Applications Using standard Bioinformatics applications.
![Page 1: Applications Using standard Bioinformatics applications.](https://reader036.fdocuments.net/reader036/viewer/2022062407/56649d425503460f94a1d9ea/html5/thumbnails/1.jpg)
Applications
Using standard Bioinformatics applications
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Introduction
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The overall plan for the regeneration of high quality annotation information as
contained in the EMBL disk-file ISTN501
figWHAT.eps
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Scientific Background ToMer Operon
● Function
● Genetic Structure and Regulation
● Mobility Of The Mer Operon
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The principal proteins and their functions
figPRINCIPLE.eps
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Downloading The Raw DNA Sequence
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Initial BLAST Sequence Similarity Search
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Maxim 18.1
With BLAST scores, up is down and lower is better
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http://opal.biology.gatech.edu/GeneMark/
GeneMark
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The web-based interface to GeneMark as running at EBI
figEBIGENEBANK.eps
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Using BLAST to identify specific sequences
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Dealing with false negatives and missing proteins
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Over predicted genes and false positives
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http://www.expasy.org/swissmod/
Structural Prediction With SWISS-MODEL
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Maxim 18.2
The major limitation of ``homology modelling'' is that homology to a known structure is needed
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Alternatives to homology modelling
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Modelling with SWISS-MODEL
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The SWISS-MODEL predicted structure of ORF2/MerP
figORF2MERP.eps
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The SWISS-MODEL predicted structure of ORF2/MerP, second version
figORF2MERP2.eps
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The SWISS-MODEL predicted structure of ORF3/MerA (A)
figORF3MERAA.eps
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The SWISS-MODEL predicted structure of ORF3/MerAB
figORF3MERAB.eps
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The SWISS-MODEL predicted structure of ORF6/TNR5
figORF6TNR5.eps
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DeepView as a Structural Alignment Tool
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The ORF2 and ORF3_A structures loaded into DeepView prior to structural
alignment
figDEEPVIEW.eps
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DeepView's Iterative Magic Fit dialogue box
figDEEPVIEWDIALOG.eps
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Structural Alignment created using the DeepView's Iterative Magic Fit facility
figDEEPVIEWEXAMPLE.eps
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Selecting the current ``layer'' in DeepView
figDEEPLAYER.eps
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Possible Explanation Behind MerA/HMA Duplication Event
figPOSSIBLE.eps
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The structural alignment of ORF3_B and the ``official'' Mercury Reductase X-ray
structure
figCYSTEINES.eps
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Maxim 18.3
Homology modelling can only model protein sequences similar to those which are already
known
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PROSITE and Sequence Motifs
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Maxim 18.4
Searching large datasets with non-specific, short sequence fragments results in many false
positives
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http://www.expasy.org/prosite/
http://www.ebi.ac.uk/interpro/
http://www.geneontology.org
● http://www.kegg.org
Using PROSITE patterns and matrices
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Phylogenetics
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A look at the HMA domain of MerA and MerP
------------------------------- -------------------------------SWISS-PROT IDs of MerP Proteins SWISS-PROT IDs of MerA Proteins------------------------------- -------------------------------MERP_ACICA MERA_ACICAMERP_ALCSP MERA_ALCSPMERP_PSEAE MERA_BACSRMERP_PSEFL MERA_ENTAGMERP_SALTI MERA_PSEAEMERP_SERMA MERA_PSEFLMERP_SHEPU MERA_SERMAMERP_SHIFL MERA_SHEPUMERA_SHIFLMERA_STAEPMERA_STRLIMERA_THIFE------------------------------- -------------------------------
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The multiple sequence alignment of the example proteins
figLISTMERAMERP.eps
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The EBI's tree graphical display
figTREE.eps
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Maxim 18.5
Whenever you make a statement, call for more research (money)!
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Maxim 18.6
Database annotation is hard to do well, so be prepared to update it on a regular basis
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Maxim 18.7
Automation can be very helpful when creating annotation, but to achieve the highest quality,
humans are needed to make some value judgments
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Maxim 18.8
Conclusions are based on the available data which, in this case, is the database annotation
(which may or may not be current)
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Where To From Here?