SCAN2a

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.