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SeqMatchNW-P |
The program implements Needleman-Wunsch algorithm to produce a global alignment of two protein 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.
Program is provided with viewer.
L:153 Sequence MYOGLOBIN MAP TURTLE
vs. 19 Base sequences [C:\Documents and Settings\My Documents\MolQuestWorkSpace\example_data\SeqMatchNW-P\seq1.set.fa].
Total 19 sequences produce 19 significant alignment(s).
[DD] 7, S: 28.714, L: 153 MYOGLOBIN CHICKEN
[DD] 17, S: 27.56, L: 153 MYOGLOBIN HUMAN
[DD] 9, S: 27.482, L: 153 MYOGLOBIN N.AMERICAN OPOSSUM
[DD] 5, S: 26.354, L: 153 MYOGLOBIN SADDLEBACK DOLPHIN
[DD] 8, S: 12.825, L: 146 HEMOGLOBIN BETA CHICKEN
[DD] 13, S: 12.696, L: 141 HEMOGLOBIN ALPHA NILE CROCODILE
[DD] 10, S: 12.388, L: 146 HEMOGLOBIN BETA N.AMERICAN OPOSSUM
[DD] 6, S: 12.271, L: 140 HEMOGLOBIN BETA EDIBLE FROG
[DD] 19, S: 12.226, L: 146 HEMOGLOBIN BETA HUMAN
[DD] 11, S: 11.998, L: 141 HEMOGLOBIN ALPHA BULLFROG
[DD] 14, S: 11.864, L: 141 HEMOGLOBIN ALPHA OSTRICH
[DD] 12, S: 11.533, L: 146 HEMOGLOBIN BETA NILE CROCODILE
[DD] 15, S: 11.521, L: 141 HEMOGLOBIN ALPHA EASTERN GRAY KANGAROO
[DD] 18, S: 11.401, L: 141 HEMOGLOBIN ALPHA HUMAN
[DD] 16, S: 11.095, L: 142 HEMOGLOBIN ALPHA ABYSSINIAN HYRAX
[DD] 2, S: 9.9819, L: 161 HEMOGLOBIN I.PARASPONIA ANDERSONII
[DD] 1, S: 9.4062, L: 146 HEMOGLOBIN VITREOSCILLA SP.
[DD] 3, S: 8.1196, L: 153 LEGHEMOGLOBIN I. YELLOW LUPIN
[DD] 4, S: 6.8096, L: 143 LEGHEMOGLOBIN I.BROAD BEAN .
****************************************************************************
[DD] Sequence: 7( 1), S: 28.714, L: 153 MYOGLOBIN CHICKEN
Summ of block lengths: 153, Alignment bounds:
On first sequence: start 1, end 153, length 153
On second sequence: start 1, end 153, length 153
Block of alignment: 1
1 P: 1 1 L: 153, G: 84.27, W: 874000, S:28.7142
1 GLSDDEWHHVLGIWAKVEPDLSAHGQEVIIRLFQVHPETQERFAKFKNLKTIDELRSSEE
||||2||44||0||2|||1|552||4||55|||40||||05||0|||1|||05|662||5
1 GLSDQEWQQVLTIWGKVEADIAGHGHEVLMRLFHDHPETLDRFDKFKGLKTPNEMKGSED
61 VKKHGTTVLTALGRILKLKNNHEPELKPLAESHATKHKIPVKYLEFICEIIVKVIAEKHP
4||||2||||1||6|||0|12||15|||||65|||||||||||||||1|7|7|||||||1
61 LKKHGATVLTQLGKILKQKGQHESDLKPLAQTHATKHKIPVKYLEFISEVIIKVIAEKHA
121 SDFGADSQAAMRKALELFRNDMASKYKEFGFQG
5||||||||||6|||||||||||||||||||||
121 ADFGADSQAAMKKALELFRNDMASKYKEFGFQG
[DD] Sequence: 17( 1), S: 27.56, L: 153 MYOGLOBIN HUMAN
Summ of block lengths: 153, Alignment bounds:
On first sequence: start 1, end 153, length 153
On second sequence: start 1, end 153, length 153
Block of alignment: 1
1 P: 1 1 L: 153, G: 81.13, W: 830000, S:27.5604
1 GLSDDEWHHVLGIWAKVEPDLSAHGQEVIIRLFQVHPETQERFAKFKNLKTIDELRSSEE
||||0||40||17|2|||1|512|||||5||||50||||0|6|0|||4||50||665||5
1 GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASED
61 VKKHGTTVLTALGRILKLKNNHEPELKPLAESHATKHKIPVKYLEFICEIIVKVIAEKHP
4||||2|||||||0|||0|14||1|5||||6||||||||||||||||1|0|75|512|||
61 LKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHP
121 SDFGADSQAAMRKALELFRNDMASKYKEFGFQG
2|||||5|2||1|||||||2||||2|||4||||
121 GDFGADAQGAMNKALELFRKDMASNYKELGFQG
....
[DD] Sequence: 7( 1), S: 28.714, L: 153 MYOGLOBIN CHICKEN
| [DD] | No sence, used for output compatibility on nucleotide sequence alignment. |
| Sequence: 7( 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 |
| MYOGLOBIN CHICKEN | Name of this query sequence |
Summ of block lengths: 153, Alignment bounds: On first sequence: start 1, end 153, length 153 On second sequence: start 1, end 153, length 153
| length | The length covered by alignment, in target and query sequences appropriately. |
Block of alignment: 1
1 P: 1 1 L: 153, G: 81.13, W: 830000, S:27.5604
Block of alignment: 1 - amount of blocks. Below each line corresponds to one block:
1 P: 1 1 L: 153, G: 81.13, W: 830000, S:27.5604
| 1 | Block number. |
| P: 1 1 | Positions of similarity block' start in target and query sequences appropriately. In this case - from the first position in both sequences. |
| L: 153 | Length of this similarity block. |
| G: 81.13 | Homology of this similarity block. |
| W: 830000 | Weight of this similarity block (the arithmetic sum of symbols' similarity calculated from the given similarity matrix). |
| S:27.5604 | Score of this similarity block. |
1 GLSDDEWHHVLGIWAKVEPDLSAHGQEVIIRLFQVHPETQERFAKFKNLKTIDELRSSEE
||||2||44||0||2|||1|552||4||55|||40||||05||0|||1|||05|662||5
1 GLSDQEWQQVLTIWGKVEADIAGHGHEVLMRLFHDHPETLDRFDKFKGLKTPNEMKGSED
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.