Program for aligning two multimegabyte-size genome sequences using a sequential search for most significant similarity regions. Program is provided with viewer.
Example of output:
L:73308 Sequence gi|455025|gb|U01317.1|HUMHBB Human beta globin region on chromosome 11 vs. 2 Base sequences [/home/apache/tmp/EP1IwQ.scan2]. [DD] Sequence: 1( 1), S: 155.86, L: 57113 gi|1418273|gb|U60902.1|OCU60902 Otolemur crassicaudatus epsilon-, gamma-, delt 1 ---------------(..)-gaattctaatctccCTCTCAACCCtacagtcacccattt( 1 attaatagttgacag(..)gcccttgactatacaCTCTCAACCCagtttccatagctga( 515 ..)ttagattaattttgtAATATTGATATTATTCCTAGAAAGCTGAGGCCTCAAGATGAT 2267 ..)aatcattagcttgacAATATTGATATTATCAATAGAAGGTTGAGGCCTAAAGGTGAT 572 AACTTTTATTttctggacttgtaat(..)aatttatgggaaaacAAGTATGTACTTTTTC 2324 GACTTTTATTcatttatttacttag(..)atttatgagaaaagaAAGTATACACTTTACC 756 TACTAAGCCATTGAAACAGGAATAACAGAACAAGATTGAAAGAATACATTTTCCGAAATT 2494 TACTAAGCCATTGAAGCATGAATAATAAAACAAGATTAAAAAATAAATTTCTCAAAAATT 816 ACTTGAGTATTATACAAAGACAAGCACGTGGACCTGGGAGgagggttattgtcca(..)t
Where:
1-st line is the header:
[DD] Sequence: 1( 1), S: 155.86, L: 57113 gi|1418273|gb|U60902.1|OCU60902 Otolemur crassicaudatus epsilon-, gamma-, delt
[DD] |
Target sequence in direct chain (D), query sequence in direct chain (D). Variants:
|
Sequence: 1( 1) |
Order number of sequence from a query set which is submitted to alignment. In brackets is an order number for alignment of this sequence (if it resulted in more than one alignment). Variants: 4( 5) - the fifth alignment of the fourth sequence from a set |
S |
Score of this alignment. |
L |
Length of this query sequence |
gi|1418273|gb|U60902.1|OCU60902 Otolemur crassicaudatus epsilon-, gamma-, delt |
Name of this query sequence |
Alignment:
1 ---------------(..)-gaattctaatctccCTCTCAACCCtacagtcacccattt( 1 attaatagttgacag(..)gcccttgactatacaCTCTCAACCCagtttccatagctga(
1 line - The target sequence itself. Capital letters correspond to blocks of similarity, lower case - not aligned regions.
1 line - The query sequence itself. Capital letters correspond to blocks of similarity, lower case - not aligned regions.