Table of contents for Bioinformatics and the cell : modern computational approaches in genomics, proteomics, and transcriptomics / by Xuhua Xia.


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Chapter I BLAST and PASTA...................
I   Introduct ion ... ....   ............._._ .........
2.  Mathematics of string matching....  ..........  ......
21      Basic concepts ........ .   ...... .. ....
3.  String-matching algorithms in FASTA and BLAST .........i
3.1    FASTA  ........... .... ..,,..................,__
3     B LA ST  ......  ... ..... ..............  ............. ... ...  16
4.  Homology search and sequence annotation....... ......... .... 20
Chapter 2 Sequence alignm.......
I  Introduction.__ ..                                   23
2.  Pairwise aligni en n. ..... ...... ................  24
2.1     Pairwise alignment with constant gap penalty,. .....  _.. .25
2,1.1  Global alignment . ...l. . .... ..... ....  25
2 .1.2  Local alignment...  ....   ....  .... ... ...... _. .29
2.1.3    The simple scoring scheme needs extension............ 30
2.2    Pairwise alignment with a similarity matrix...30
2.2.1    DNA  matrices.. ....... . . .. ................ ....  .. ...30
2,2.2    Protein  matrix  .....  ..................._..............  32
affine function  .... ... ..... ...... ..... ............... ___34
3.  Multiple sequence alignment ... .. ..... .. ...... ....38
3.1    Profile alignment. ..........                  . 38
3.2    Multiple alignment with a guide tree ............  ........41
4.  Sequence alignment with secondary structure ........43
5.  Align nucleotide sequences against amino acid sequences.,.... --44
.6.  Postscript.....-......         ....                .....47
Chapter 3 Contig assembly   ...........   ..................-49
1.  Introduction. ....  ...... .................... .............. ......  49
2.  Skeletal output of contig assembly -..... ....  .......51
3   string matching of two sequence ends ...........     56
4.  New development in contig assembly........       ...... 59