tools and datasets exploring the tools of the trade
Post on 20-Dec-2015
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Tools and Datasets
Exploring the tools of the trade
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Sequence Databases
● Understanding EMBL Entries
● Understanding SWISS-PROT Entries
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Understanding EMBL Entries
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Understanding SWISS-PROT Entries
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General Concepts and Methods
● Predictions and Validation
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Maxim 17.1
Recognise the difference between the validation of a model and the testing of it for
self-consistency
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True/False/Negative/Positive
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Maxim 17.2
Generally, False Negative predictions are considered more acceptable than False
Positives
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Assessment/Validation Procedure and Possible Outcomes
figOUTCOME.eps
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Balancing the errors
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Maxim 17.3
With False Negatives we could come back next year and find the ones we missed, and these
are preferred to False Positives, where we can waste time studying them this year, only to find out that the time was wasted. It all depends on
the circumstances
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Maxim 17.4
Sometimes all those false positives are maybe, just maybe, trying to tell you something. So, if
you aspire to a Nobel prize ...
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Using multiple algorithms to improve performance
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Maxim 17.5
Use a fast if inaccurate algorithm to protect your slow, accurate second-stage algorithm
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An overview of tRNA: 2D, 3D and Gene Structure
figTRNA.eps
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http://www.ncbi.nlm.nih.gov/Education/
Introducing Bioinformatics Tools
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http://www-igbmc.u-strasbg.fr/BioInfo/
ftp://ftp.ebi.ac.uk/pub/software
ClustalW
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ClustalX operating under Windows XP
figCLUSTALX.eps
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$ gzip -d clustalw1.83.UNIX.tar.gz
$ tar -xvf clustalw1.83.UNIX.tar
$ cd clustalw1.83
$ make
$ ./clustalw
$ ./clustalw -h
$ ./clustalw -INFILE=../MerAHMAs_MerP.swp -OUTFILE=../Mer.aln
Algorithms and Methods
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Substitution/scoring matrices
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BLAST
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Maxim 17.6
Exactly which BLAST is best depends on the circumstances
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$ cd
$ mkdir blast
$ cp blast-2.2.6-ia32-linux.tar.gz blast
$ cd blast
$ gzip -d blast-2.2.6-ia32-linux.tar.gz
$ tar -xvf blast-2.2.6-ia32-linux.tar
[NCBI]
Data="/home/michael/blast/data"
Installing NCBI-BLAST
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$ mkdir databases
$ cd databases
$ mv ../All_Mer_Proteins.fsa .
$ ../formatdb -i All_Mer_Proteins.fsa -p T -o T -n Merproteins
$ blastall -p blastp -d databases/Merproteins -i test_seq.fsa
$ sed 's/sw|/sp|/' All_Mer_Proteins.fsa > Mer_db.prot
$ ../formatdb -i Mer_db.prot -p T -o T -n Merproteins
Preparation of database files for faster searching
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$ fastacmd -d databases/Merproteins -I
$ fastacmd -d databases/Merproteins -s MERA_SHIFL
$ blastclust -d databases/Merproteins | head
The different types of BLAST search
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Where To From Here