The program implements Needleman-Wunsch algorithm to produce a global alignment of two nucleotide sequences. The approach is described in "A general method applicable to the search for similarities in the amino acid sequence of two proteins", J Mol Biol. 48(3):443-53. The Needleman-Wunsch algorithm uses dynamic programming, and is guaranteed to find the alignment with the maximum score with respect to the scoring system being used (which includes the substitution matrix and the gap-scoring scheme.
L:999 Sequence gi|1418273|gb|U60902.1|OCU60902 Otolemur crassicaudatus epsilon-, gamma-, delta-, and beta-globin genes, complete cds, and eta-globin pseudogene
vs C:\Documents and Settings\My Documents\MolQuestWorkSpace\example_data\SeqMatchNW-N\1\seq1.fa
Total 1 sequences produce 1 significant alignment(s).
[DD] 1, S: 14.962, L: 292 gi|455025|gb|U01317.1|HUMHBB Human beta globin region on chromosome 11
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[DD] Sequence: 1( 1), S: 14.962, L: 292 gi|455025|gb|U01317.1|HUMHBB Human beta globin region on chromosome 11
Summ of block lengths: 251, Alignment bounds:
On first sequence: start 1, end 940, length 940
On second sequence: start 2, end 292, length 291
Block of alignment: 37
1 P: 1 2 L: 1, G: 100.00, W: 5, S:1
2 P: 33 3 L: 4, G: 100.00, W: 20, S:2.82843
3 P: 41 7 L: 4, G: 100.00, W: 20, S:2.82843
4 P: 58 11 L: 3, G: 100.00, W: 15, S:2.32379
5 P: 101 14 L: 7, G: 71.43, W: 17, S:2.50185
6 P: 117 26 L: 13, G: 76.92, W: 38, S:4.02492
7 P: 141 39 L: 3, G: 100.00, W: 15, S:2.32379
8 P: 149 42 L: 3, G: 100.00, W: 15, S:2.32379
9 P: 168 55 L: 9, G: 77.78, W: 27, S:3.30748
10 P: 201 64 L: 13, G: 61.54, W: 20, S:2.83235
11 P: 231 77 L: 4, G: 100.00, W: 20, S:2.82843
12 P: 245 81 L: 3, G: 100.00, W: 15, S:2.32379
13 P: 255 84 L: 4, G: 100.00, W: 20, S:2.82843
14 P: 273 88 L: 8, G: 75.00, W: 22, S:2.92119
15 P: 290 98 L: 8, G: 62.50, W: 13, S:2.19089
16 P: 304 106 L: 11, G: 90.91, W: 46, S:4.64372
17 P: 320 121 L: 10, G: 70.00, W: 23, S:3
18 P: 346 139 L: 9, G: 77.78, W: 27, S:3.30748
19 P: 368 148 L: 6, G: 83.33, W: 21, S:2.85774
20 P: 378 154 L: 10, G: 80.00, W: 32, S:3.66667
21 P: 392 164 L: 4, G: 100.00, W: 20, S:2.82843
22 P: 411 171 L: 8, G: 75.00, W: 22, S:2.92119
23 P: 426 179 L: 9, G: 66.67, W: 18, S:2.61116
24 P: 467 188 L: 10, G: 90.00, W: 41, S:4.33333
25 P: 482 198 L: 5, G: 80.00, W: 16, S:2.4004
26 P: 502 203 L: 3, G: 100.00, W: 15, S:2.32379
27 P: 515 207 L: 12, G: 83.33, W: 42, S:4.32049
28 P: 547 226 L: 12, G: 75.00, W: 33, S:3.70328
29 P: 621 238 L: 7, G: 85.71, W: 26, S:3.27165
30 P: 641 245 L: 7, G: 71.43, W: 17, S:2.50185
31 P: 653 252 L: 3, G: 100.00, W: 15, S:2.32379
32 P: 706 255 L: 6, G: 83.33, W: 21, S:2.85774
33 P: 727 261 L: 17, G: 70.59, W: 40, S:4.10605
34 P: 888 278 L: 5, G: 80.00, W: 16, S:2.4004
35 P: 907 283 L: 5, G: 100.00, W: 25, S:3.27327
36 P: 929 288 L: 2, G: 100.00, W: 10, S:1.73205
37 P: 938 290 L: 3, G: 100.00, W: 15, S:2.32379
1 -AttaatagttgacagggatttacactaatgttATTCatcaTAATatgggatgtatcgCT
.|...............................||||....||||.............||
1 gA-------------------------------ATTC----TAAT-------------CT
60 Cattgttgtttatttg(..)gaagaaaagttaaatCATTTCAttctttgtgAAAGACATC
|...............(..)...............|0|0|||.........|0||0||0|
13 C---------------(..)---------------CCTCTCAaccct----ACAGTCACC
126 CATTaacccaccctcTGGatcacTATgctttagcagtttcaaTGTAGGCTAgtaagcctg
||||...........|||.....|||................|||0|0|||.........
35 CATT-----------TGG-----TATattaaagatg------TGTTGTCTA---------
....
[DD] Sequence: 1( 1), S: 14.962, L: 292 gi|455025|gb|U01317.1|HUMHBB Human beta globin region on chromosome 11
| [DD] | Target sequence in direct chain (D), query sequence in direct chain (D). Variants:
[DR] - target sequence in direct chain (D), query sequence in reverse chain (R). [RD] - target sequence in reverse chain (R), query sequence in direct chain (D). [RR] - target sequence in reverse chain (R), query sequence in reverse chain (R). |
| 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|455025|gb|U01317.1|HUMHBB Human beta globin region on chromosome 11 | Name of this query sequence |
Summ of block lengths: 251, Alignment bounds: On first sequence: start 1, end 940, length 940 On second sequence: start 2, end 292, length 291
| length | The length covered by alignment, in target and query sequences appropriately. |
Block of alignment: 37
1 P: 1 2 L: 1, G: 100.00, W: 5, S:1
2 P: 33 3 L: 4, G: 100.00, W: 20, S:2.82843
Block of alignment: 37 - Number of blocks in this alignment.
Each line below defines an appropriate block. Detailed description of a line from this list is shown further:
2 P: 33 3 L: 4, G: 100.00, W: 20, S:2.82843
| 2 | Block number. |
| P: 33 3 | Positions of similarity block' start in target and query sequences appropriately. |
| L: 4 | Length of this similarity block. |
| G: 100.00 | Homology of this similarity block. |
| W: 20 | Weight of this similarity block (the arithmetic sum of symbols' similarity calculated from the given similarity matrix). |
| S:2.82843 | Score of this similarity block. |
60 Cattgttgtttatttg(..)gaagaaaagttaaatCATTTCAttctttgtgAAAGACATC
|...............(..)...............|0|0|||.........|0||0||0|
13 C---------------(..)---------------CCTCTCAaccct----ACAGTCACC
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.