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Tools and Datasets Exploring the tools of the trade.

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Presentation on theme: "Tools and Datasets Exploring the tools of the trade."— Presentation transcript:

1 Tools and Datasets Exploring the tools of the trade

2 Sequence Databases ● Understanding EMBL Entries ● Understanding SWISS-PROT Entries

3 Understanding EMBL Entries

4 Understanding SWISS-PROT Entries

5 General Concepts and Methods ● Predictions and Validation

6 Maxim 17.1 Recognise the difference between the validation of a model and the testing of it for self-consistency

7 True/False/Negative/Positive

8 Maxim 17.2 Generally, False Negative predictions are considered more acceptable than False Positives

9 Assessment/Validation Procedure and Possible Outcomes figOUTCOME.eps

10 Balancing the errors

11 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

12 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...

13 Using multiple algorithms to improve performance

14 Maxim 17.5 Use a fast if inaccurate algorithm to protect your slow, accurate second-stage algorithm

15 An overview of tRNA: 2D, 3D and Gene Structure figTRNA.eps

16 http://www.ncbi.nlm.nih.gov/Education/ Introducing Bioinformatics Tools

17 http://www-igbmc.u-strasbg.fr/BioInfo/ ftp://ftp.ebi.ac.uk/pub/software ClustalW

18 ClustalX operating under Windows XP figCLUSTALX.eps

19 $ 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

20 Substitution/scoring matrices

21 BLAST

22 Maxim 17.6 Exactly which BLAST is best depends on the circumstances

23 $ 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

24 $ 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

25 $ fastacmd -d databases/Merproteins -I $ fastacmd -d databases/Merproteins -s MERA_SHIFL $ blastclust -d databases/Merproteins | head The different types of BLAST search

26 Where To From Here


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