Scoring Matrix
الثلاثاء, 24 يناير 2017 13:34

ضمن جدول محاضرات الموسم الثقافي لقسم التقنيات الاحيائية / كلية العلوم/ جامعة بغداد ، القى الاستاذ المساعد الدكتور ايهاب داود سلمان محاضرة علمية بعنوان Scoring Matrix على قاعة المناقشات الرئيسية في القسم .

 

Abstract:

In bioinformatics , scoring matrix mean give value to matrix , which considered a  key element in evaluating the quality of a pairwise alignment.

A pairwise alignment mean: Comparison of 2 sequences – nucleotide or protein seypquences , We have three types of pairwise alignments:-

1-Global alignment: which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming.

2-local alignment: Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith–Waterman algorithm is a general local alignment method also based on dynamic programming.

3-Multiple sequence alignment: is an extension of pairwise alignment to incorporate more than two sequences at a time. It often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related.

Some time there are once more type of alignment such as semiglobal or "glocal" (short for global-local) methods, attempt to find the best possible alignment that includes the start and end of one or the other sequence. It was used when one sequence is short (for example a gene sequence) and the other is very long (for example a chromosome sequence). In that case, the short sequence should be globally aligned but only a local alignment is desired for the long sequence.

In bioinformatic , scoring matrix mean give value to matrix , which considered a  key element in evaluating the quality of a pairwise alignment.

A pairwise alignment mean: Comparison of 2 sequences – nucleotide or protein seypquences , We have three types of pairwise alignments:-

1-Global alignment: which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. A general global alignment technique is the Needleman–Wunsch algorithm, which is based on dynamic programming.

2- local alignment: Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith–Waterman algorithm is a general local alignment method also based on dynamic programming.

3- Multiple sequence alignment: is an extension of pairwise alignment to incorporate more than two sequences at a time. It often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related.

Some time there are once more type of alignment such as semiglobal or "glocal" (short for global-local) methods, attempt to find the best possible alignment that includes the start and end of one or the other sequence. It was used when one sequence is short (for example a gene sequence) and the other is very long (for example a chromosome sequence). In that case, the short sequence should be globally aligned but only a local alignment is desired for the long sequence.

 


A                                                                                                                                          B

D         

C

F                E


 

DeanCV2014

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