YASS : genomic similarity search 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
(files)

(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)

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 first sequence)
Display quick alignments and statistics [?]
Mask lowercase (do not "index" lowercase letters, they are still used during "extension")
Sort [?]

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

Seed parameters

Seed pattern [?] (file)	new: faster (but with lower sensitivity) → select MoW seeds (end of this list)
Hit criterion strategy [?]

Sequence mutation parameters

Indels [?]	%
Mutation [?]	%

Gapped alignment post-processing

Window range [?]	bp, bp
Window incr [?] (0:disable post-processing)	x factor

Low complexity filter

Entropy (tri-nucl.) [?]

bits