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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.

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