SURF tutorial

SURF TUTORIAL 1 Prelude This document presents the SURF steps from instance creation to batch feature detection. You may add de SURF bin directory to your PATH variable (.cshrc. file). setenv PATH ${PATH}:/project/surf/bin We will assume in this tutorial that SURF is installed in /project directory and that the studied instance will be called ‘MyProject. SURF can process chromatogram, fasta, dbest and embl batches, we will use a chromatogram batch in that tutorial in order to see the whole SURF functionalities. 2 Instance creation Surf provides an instance creation program called ‘create_instance.pl’ which: - create database schema (create db itself if you are granted) - install a file system (‘MyInstance’ directory) under /projectsurf/data/ We will use bovine sequences, so species parameter will be equal to ‘bos taurus’ create_instance.pl –-name MyInstance --species ‘bos taurus’ species parameter is used by RepeatMasker in order to use NCBI taxonomy data, so you may use full taxon syntax (eg bos taurus, sus scrofa). Do not forget quotes in order to keep any blanks into parameters. Create_instance.pl installs some fasta banks into instance file system (/project/surf/data/MyInstance/banks). These banks are symbolic links to a SURF global banks repository (/project/surf/data/banks) but some of these banks (mito.fasta and ribo.fasta) are species specific so you may update theses links to the dedicated files. We assume that mito_cattle.tfa and ...