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Tutorial

Synthviewer : viewer of homologies between two proteic or nucleic sequences
You can see in one image the homologies between sequences A and B, A and C, B and C, Y and Z...

The data file is a tabulated text file (see an example) that describes your sequences and their homologies.
Lines in this file can be unordered.

1- Sequences description
You must describe each sequence with the tag "locus". For example you want to see comparisons between sequences A (100000 nt) and B (780000 nt). Your datafile must contain :

seqA	locus	1	100000
seqB	locus	1	78000

If, as in the example, seqA is a fragmented BAC like newbler contigs, write as many locus as fragments for this bac. The graph will show them as a fragmented line according to the positions you give with the locus tag.
Don't forget to give them intelligent coordinates, else they will overlap or will have irregulate space between them.

seqA	locus	1	20000
seqA	locus	25000	105000
seqB	locus	1	78000

Now seqA is splitted in two parts.

You can describe regions on the sequences. Regions are visualised with boxes on the sequence line. In this purpose, use the tag "region" ang give a name for each of them.

seqA	locus	1	20000
seqA	locus	25000	105000
seqB	locus	1	78000
seqA	region	1000	7000	regionA1
seqA	region	27000	32500	regionA2
seqB	region	55000	78000	regionB

You can describe genes on the sequences. Genes are visualised with a black line on the sequence. In this purpose, use the tag "gene" ang give a name and a strand (+/-) for each of them.
The description of a gene is very simple and isn't adapted for structures (intron/exon/utr). Genes on strand + are above the sequence line. Genes on strand - are bellow the sequence line. They are black colored.
You can use also the tag marker, to show "special" genes, in green.

seqA	locus	1	20000
seqA	locus	25000	105000
seqA	gene	1005	2070	geneA1	+
seqA	gene	28204	31540	geneA2	-
seqA	marker	26600	27900	Marker1	-
seqA	region	1000	7000	regionA1
seqA	region	27000	32500	regionA2

seqB	locus	1	78000
seqB	region	55000	78000	regionB

2- Description of the homologies
Use the tag "align" followed with an integer to described a comparison between two sequences.
align1 and align2 will generate two comparison views.
Those lines must first refer to the sequence at the top of the comparison in the picture, with the coordinates of the aligned part, and then to the sequence at the bottom of the comparison, with coordinates of the aligned part.
The last field of those lines is the direction of the alignment (+ for same direction or - for opposite direction).

seqA	locus	1	20000
seqA	locus	20200	105000
seqA	gene	1005	2070	geneA1	+
seqA	gene	28204	31540	geneA2	-
seqA	region	1000	7000	regionA1
seqA	region	27000	32500	regionA2

seqB	locus	1	78000
seqB	region	55000	78000	regionB

#seqA is the top sequence, seqB the bottom sequence
seqA	align1	1	600	seqB	100	740	+
seqA	align1	25500	40000	seqB	4000	18950	+
seqA	align1	27800	31500	seqB	54800	58900	-

To add another comparison view, add new align lines like this (a seqC has been added and compared to seqA).

seqA	locus	1	20000
seqA	locus	20200	105000
seqA	gene	1005	2070	geneA1	+
seqA	gene	28204	31540	geneA2	-
seqA	region	1000	7000	regionA1
seqA	region	27000	32500	regionA2

seqB	locus	1	78000
seqB	region	55000	78000	regionB

seqC	locus	1	80000
#seqA is the top sequence, seqB the bottom sequence
seqA	align1	1	600	seqB	900	1500	+
seqA	align1	25500	40000	seqB	4000	18950	+
seqA	align1	27800	31500	seqB	54800	58900	-

seqA	align2	25000	41000	seqC	3500	19950	+
seqA	align2	27800	31500	seqC	54800	58900	-

Comparison lines can have an optional field, for example, to write the %identity of an alignment :
seqA	align1	1	600	seqB	900	1500	+	60%
seqA	align1	25500	40000	seqB	4000	18950	+	95%
seqA	align1	27800	31500	seqB	54800	58900	-	67%

seqA	align2	25000	41000	seqC	3500	19950	+	89%
seqA	align2	27800	31500	seqC	54800	58900	-	56%