added documentation

README.md

@@ -25,10 +25,36 @@ Install the detector module
 
 ### Commands
 
-TODO
+First, you need to create a blast database from a set of known transposable element proteins. First collect sequences of
+such elements in fasta format and store them in one directory. Note that all files should have the extension .fasta. 
+Alternatively, the files in *./TE_DB/* can be used. For more details how these were prepared read the file 
+[here](TE_DB/README.md).
 
-  * Collect sequences for known protein coding transposable elements.
-  * Script to initiate pipeline (build blast DB)
-  * Script to blast fasta files (with support for a cluster)
-  * Script to parse output and report potential TEs
+Create the blast DB using the command below
+
+    detector build ./TE_DB/ known_te_db
+
+This command will pick up all fasta-files in the TE_DB folder, concatenate them and build a blast database named 
+known_te_db.
+
+Next, a fasta-file (with protein sequences) should be basted against the newly created database with known transposable
+element proteins.
+
+    detector blast species_peptides.fasta known_te_db species_blast_output
+
+ This command will blast a protein fasta-file species_peptides.fasta against known_te_db (created in the previous step).
+ The output will be stored in species_blast_output
+
+ Finally, from the output, sequences similar to known transposable element proteins can be extracted using the analyze 
+ command below.
+
+     detector analyze species_blast_output species_putative_te.lst
+     
+ The file species_putative_te.lst will be created if putative transposable element proteins are found.
+
+
+# TODO
+
+  * Add support for cluster
+  * Parameters for analyze (desired cutoff) + determine good thresholds
   * Script to remove TEs from initial input producing a final *clean* fasta file