sRNAblast:

Different types of input can be provided: fastq, sra, read/count and fasta format.
The files can be provided as plain text (fastq, read/count and fasta) or compressed with gzip (*.gz extension). Please try whenever possible upload *.gz files.
Please note that sRNAbench infers the file format by means of the extension. unknown extensions are treated as read/count format. For example sample.gz would be treated as read/count format file. The program will fail if the file format is incorrectly inferred.
The recognized extensions are:
fasta: fa, fasta, fa.gz, fasta.gz
read/count: rc, rc.gz
sra: sra
fastq: fastq.gz, fastq, fq, fq.gz, FASTQ, FASTQ.gz, fastQ, fastQ.gz

File format explanation:
read/count
read/count format is tab separated with two columns: the read sequence separated by the read count (number of times this read was sequenced)
read read count
ATTACG… 3000
GCATT… 2500

fasta format:
>readID#3000
ATTACG…
>readID#2500

Note that spaces between the readID and the read count are also allowed.

Users can add here specific option for each of the programs selected.
Please note: Users must read the documention of each program before add any parameters, since the parameters won't be controlled or checked by this application any incorrect parameter will cause errors in the ouput or even the failure of the job lauched.

--mimic <1> search for target mimics (default 0)
--score <value> score cutoff (default 4)
--mfe <value> mfe ratio cutoff (default 0.7)

--score score cutoff
--mfe mfe ratio cutoff

-sc S Set score threshold to S [DEFAULT: 140.0]
-en -E Set energy threshold to -E kcal/mol [DEFAULT: 1.0]
-scale Z Set scaling parameter to Z [DEFAULT: 4.0]
-strict Demand strict 5' seed pairing [DEFAULT: off]

Alignment parameters:
-go -X Set gap-open penalty to -X [DEFAULT: -4.0]
-ge -Y Set gap-extend penalty to -Y [DEFAULT: -9.0]

General Options:
-out file Output results to file [DEFAULT: off]
-quiet Output fewer event notifications [DEFAULT: off]
-trim T Trim reference sequences to T nt [DEFAULT: off]
-noenergy Do not perform thermodynamics [DEFAULT: off]

-ts target penalty score, lower is better (0-5)
default = 2.5
-fp 5 prime boundary of essential sequence (1-2)
default = 2
-tp 3 prime boundary of essential sequence (7-31)
default = 17
-gl position after which with gap/bulge permit (0-30), 0 means no gap/bulge permitted
default = 17
-p number of processors use
default = 1
-gn number of gaps/bulges permitted (0-5)
default = 1

-s,--seed set seed as a requirement
-threshold sens, spec or any number in (0,1). Default is sens
-transcripts transcript fasta file

-flank_up <bp>
-flank_down <bp>: Flank requirement in basepairs (default: zero for both)
-ddG_context <bp>: Number of bases upstream and downstream for target site that are taken into account when folding the UTR (default: 70)
-prefix <string>: Add the string as a prefix to the output files (pita_results.tab and ext_utr.stab)
-gxp: Produce a gxp (Genomica project file) output file.
-l <num1-num2>: Search for seed lengths of num1,...,num2 to the MicroRNA (default: 6-8)
-gu <nums>: Lengths for which G:U wobbles are allowed and number of allowed wobbles. Format of nums: <length;num G:U>,<length;num G:U>,... (default: 6;0,7;1,8;1)
-m <nums>: Lengths for which mismatches are allowed and number of allowed mismatches Format of nums: <length;num mismatches>,<length;num mismatches>,...(default: 6;0,7;0,8;1)
-loop <nums>: Lengths for which a single loop in either the target or the microrna is allowed. Format of nums: <length>,<length>,... (default: none)