SeqMatch-P

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 HUMAN 
vs C:\Documents and Settings\My Documents\MolQuestWorkSpace\example_data\SeqMatch-P\seq1.fa
Total 1 sequences produce 1 significant alignment(s).

[DD]       1, S:      21.664, L:      146 HEMOGLOBIN BETA NILE CROCODILE
****************************************************************************
[DD] Sequence:       1(      1), S:      21.664, L:      146 HEMOGLOBIN BETA NILE CROCODILE
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 vhltpeEKsavtaLWGKVNVdevGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
          ......||.....||0||7|...|||||0|8|9||||07|9||7|||8|000|9|0|0||
        1 asfdphEKqligdLWHKVDVahcGGEALSRMLIVYPWKRRYFENFGDISNAQAIMHNEKV

       61 KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
          7|||||||07|08070|||08800||0||7|||8|||||||||8|||79890|||0|90|
       61 QAHGKKVLASFGEAVCHLDGIRAHFANLSKLHCEKLHVDPENFKLLGDIIIIVLAAHYPK

      121 EFtppvqAAYQKVVagVAnALAHKYH
          8|.....|||||7|..||.|||07||
      121 DFglechAAYQKLVrqVAaALAAEYH
....

Where:

1-st line is the header:


[DD] Sequence:       1(      1), S:      21.664, L:      146 HEMOGLOBIN BETA NILE CROCODILE
[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 NILE CROCODILE 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 vhltpeEKsavtaLWGKVNVdevGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
          ......||.....||0||7|...|||||0|8|9||||07|9||7|||8|000|9|0|0||
        1 asfdphEKqligdLWHKVDVahcGGEALSRMLIVYPWKRRYFENFGDISNAQAIMHNEKV

1 line - The target sequence itself. Capital letters correspond to blocks of similarity, lower case - not aligned regions.
2 line - Separator line. Separator line symbols: "|" - perfect coincidence between symbols. Figures means the degree of symbols' similarity. Vary from 0 up to 9. 0 - no similarity, 9 - maximal similarity.
3 line - The query sequence itself. Capital letters correspond to blocks of similarity, lower case - not aligned regions.