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 -
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%