diff test-data/tblastN/readme/README.md @ 1:fb5e60d4d18a draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty

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+Conversion of NCBI BLAST+ tblastn results to PSL format
+=======================================================
+Wilson Leung <[e-mail]>
+
+Last Update: 04/24/2016
+
+
+Version information
+-------------------
+* Kent source tree: v324
+* NCBI BLAST+: BLAST 2.2.30+
+
+Data sources
+-------------------
+For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the *D. melanogaster* *ci* gene in contig1. The protein sequences are available through [FlyBase](http://flybase.org/cgi-bin/getseq.html?source=dmel&id=FBgn0004859&chr=4&dump=PrecompiledFasta&targetset=translation).
+
+* Dbia3.fa = contig1 sequence in the Dbia3 asssembly
+* ci.pep = Protein sequences for the three isoforms of the *ci* gene in *D. melanogaster*
+
+Conversion protocol
+-----------------------
+1. Create BLAST database for the assembly
+```
+makeblastdb -in Dbia3.fa -dbtype nucl
+```
+
+2. Perform tblastn search and output results in XML format
+```
+tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2
+```
+
+3. Convert results into PSL format
+```
+blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl
+```
+
+4. Convert PSL output into BED format
+```
+pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed
+```
+
+Output files
+-----------------------
+* tblastn_Dbia3_ci.xml = tblastn results in XML format
+* tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format
+* tblastn_Dbia3_ci.xml.bed = tblastn results in BED format
+
+