Program for aligning two aminoacid sequences using a sequential search for most significant similarity regions. Program is provided with viewer.
Example of output:
L:146 Sequence HEMOGLOBIN BETA NILE CROCODILE vs /home/apache/tmp/glWcq4.scan2 [DD] Sequence: 1( 1), S: 21.664, L: 146 HEMOGLOBIN BETA HUMAN Summ of block lengths: 124, Alignment bounds: On first sequence: start 7, end 146, length 140 On second sequence: start 7, end 146, length 140 Block of alignment: 6 1 P: 7 7 L: 2, G: 100.51, W: 10, S:2.64676 2 P: 14 14 L: 7, G: 83.27, W: 20, S:5.05147 3 P: 24 24 L: 99, G: 78.57, W: 225, S:20.0317 4 P: 128 128 L: 7, G: 94.76, W: 30, S:5.80101 5 P: 137 137 L: 2, G: 92.46, W: 8, S:2.4219 6 P: 140 140 L: 7, G: 82.12, W: 19, S:4.97651 1 asfdphEKqligdLWHKVDVahcGGEALSRMLIVYPWKRRYFENFGDISNAQAIMHNEKV 1 vhltpeEKsavtaLWGKVNVdevGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV 61 QAHGKKVLASFGEAVCHLDGIRAHFANLSKLHCEKLHVDPENFKLLGDIIIIVLAAHYPK 61 KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK ...
Where:
1-st line is the header:
[DD] Sequence: 1( 1), S: 21.664, L: 146 HEMOGLOBIN BETA HUMAN
[DD] |
No sence, used for output compatibility on nucleotide sequence alignment. |
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 |
HEMOGLOBIN BETA HUMAN |
Name of this query sequence |
Additional information about alignment:
Summ of block lengths: 124, Alignment bounds: On first sequence: start 7, end 146, length 140 On second sequence: start 7, end 146, length 140
length |
The length covered by alignment, in target and query sequences appropriately. |
List of alignment blocks:
Block of alignment: 6 1 P: 7 7 L: 2, G: 100.51, W: 10, S:2.64676 2 P: 14 14 L: 7, G: 83.27, W: 20, S:5.05147
Block of alignment: 6 - Number of blocks in this alignment.
Each line below defines an appropriate block. Detailed description of a line from this list is shown further:
1 P: 7 7 L: 2, G: 100.51, W: 10, S:2.64676
1 |
Block number. |
P: 7 7 |
Positions of similarity block' start in target and query sequences appropriately. In this case - from the seventh position in both sequences. |
L: 2 |
Length of this similarity block. |
G: 100.51 |
Homology of this similarity block. |
W: 10 |
Weight of this similarity block (the arithmetic sum of symbols' similarity calculated from the given similarity matrix). |
S:2.64676 |
Score of this similarity block. |
Alignment:
1 asfdphEKqligdLWHKVDVahcGGEALSRMLIVYPWKRRYFENFGDISNAQAIMHNEKV 1 vhltpeEKsavtaLWGKVNVdevGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
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.