RJE_APOLLO is a wrapper for GABLAM that peforms a limited number of focused GABLAM functions and adds some additional
data cleanup and outputs. It is primarily designed for use as part of the SLiMSuite REST servers as a way to search
the WebApollo genome servers of the Edwards Lab. See the REST output and Apollo webserver for more details.
Version 0.2.0 added the option of running exonerate rather than BLAST+, which will probably become the default option
on the server.
seqin=FASFILE : Fasta file of input sequences to search against genome 
genome=FASFILE : Fasta file of genome to search against
qrytype=X : Type of seqin query file (cds/transcript/dna/protein) [
basefile=FILE : Root of output files [
maxqry=INT : Maximum number of sequences allowed for seqin [
GABLAM Search Options
blaste=NUM : E-Value cut-off for BLAST searches (BLAST -e X) [
tophits=INT : Sets max number of BLAST hits returned (blastb and blastv) [
localmin=INT : Minimum length of local alignment to output to local stats table [
localidmin=PERC : Minimum local %identity of local alignment to output to local stats table [
keepblast=T/F : Whether to keep the blast results files rather than delete them [
blasttask=X : Flavour of blast to use (BLAST -task X) (NOTE: blastn default is megablast) [
exonerate=T/F : Whether to use exonerate in place of GABLAM. Can also set
exopt=X : Additional exonerate options 
webapollo=URL : URL base for Web Apollo genome browser [https://edwapollo.babs.unsw.edu.au/apollo-2.0.8/]
genomeid=X : Genome identifier code for Web Apollo genome browser (with optional .public), or SPEC:ID list 
tracks=LIST : Comma separated list of tracks to display for WebApollo server 
exoneratebin=PATH : Path to exonerate program bin (can be '' if added to environment path) [
History Module Version History
# 0.0.0 - Initial Compilation.
# 0.1.0 - Initial Working Version.
# 0.1.1 - Modified HTML output.
# 0.2.0 - Added basic exonerate output.
# 0.3.0 - Added transcript query type.
# 0.4.0 - Added MaxQry=INT : Maximum number of sequences allowed for seqin 
# 0.5.0 - Added QryDesc to exonerate GFF output.
# 0.6.0 - Added cdict parsing to genomeid.
# 0.6.1 - Debugging genomeID dict and fixed cdict parsing bug.
# 0.6.2 - Added QryDesc to HTML output.
# 0.6.3 - Made protein synonym for prot as qrytype.
rje_apollo REST Output formats
for program documentation and options. A plain text version is accessed with
can be used to retrieve individual parts of the output, matching the tabs in the default
) output. Individual
elements can also be parsed from the full (
) server output,
which is formatted as follows:
... contents for OUTFMT section ...
General REST Outputs
= Reduced summary table with links to WebApollo genome
= Input search sequence [fasta]
= One line summary of hits per query [tdt]
= Local alignments table [tdt]
= Local alignments table in GFF3 format [gff3]
= Local alignments table, reduced to non-overlapping query regions [tdt]
Exonerate REST Outputs
= Exonerate alignment [txt]
= Exonerate GFF2 output [gff2]
= Exonerate cigar output [txt]
= Fasta file of hit sequences [fasta]
= Fasta file of translated hits (CDS or protein only) [fasta]
BLAST+ REST Outputs
= Full GABLAM summary table of each Query-Hit pair [tdt]
= Raw BLAST results [txt]
= Local BLAST+ alignments table, reduced to non-overlapping query regions, in GFF3 format [gff]
= Local BLAST alignments table in SAM alignment format (blastn only) [sam]
= BLAST results formatted in query assembly
= Query sequence aligned to consensus for each hit from QBLAST [fasta]
= Degapped consensus hits from QBLAST [fasta]
The Apollo server can be found here: http://www.slimsuite.unsw.edu.au/servers/apollo.php. Alternatively, you can run it using the input form, below.
This server allows simple Exonerate or BLAST+ searches of DNA, CDS or protein sequences against one of our WebApollo genomes. Select the genome to search and the WebApollo instance to generate links for. Optionally, tracks to display can be listed under Advanced Options. Private genomes will need a
password for access. This password will also be required to access the REST server results.
Note: some genomes may have multiple WebApollo annotations. It is the genome status, not the Apollo status that determines password requirements. If no WebApollo ID is selected, no links table will be generated - other search results will still be returned.