YASS :: genomic DNA alignment tool

Data [?]

(1/2) Select the genomic (DNA/RNA) sequence(s) to be compared with YASS (1 sequence selected = self-comparison)

Upload your sequence(s)

choose your file(s), then press select

And/Or
And/Or
Paste your sequence(s)

copy/paste your sequence(s), then press select

And/Or
And/Or
Use proposed sequence(s)

choose the species/database (hold down [⇧ shift] key + type first letters) and the sequence, then press select

(2/2) Please check the selected DNA sequence(s), then run YASS

Selected DNA sequence(s)
(small fasta/multifasta file with few chunks)
(fasta/multifasta file)


If you use this program, please cite : L. Noe, G. Kucherov, YASS: enhancing the sensitivity of DNA similarity search, 2005, NAR, 33(2)

Parameters (optional) [?]

Scoring system
Scoring matrix (match,transversion,transition,other)
Gap costs (opening,extension) ,
E-value threshold
X-drop threshold
Display
DNA strain:process forward, reverse complement or both reads of the first sequence
Display quick alignments and statistics [?] : display quick alignments along with some statistics
Mask lowercase : do not "index" lowercase letters (still used during "extension")
Sorting :




Advanced parameters (optional) [?]

these options are provided for advanced use of the YASS tool (see the readme file)

Search parameters
Seed pattern [?]: (file)
Hit criterion strategy [?]
Window range [?] bp, bp
Window incr [?] x factor
Sequence mutation parameters
Indels [?] %
Mutation [?] %
Filter
Entropy filter (tri-nucl.) [?] bits