Index practica bio-informatica

Hoofdstuk Onderwerpen Slides Verbetering
pagina's
P1: Databases and  NCBI Databases  4-30  3-11
alignment o Gene database  4-8  3
o GenBank  9-15  6
 Accession number
 Version number
 FASTA file
o All databases  8
o dbSNP (grootste databank voor nucleotide  16  9
variatie)  17-21
 Uniprot (! Protein databases)  12-15
o Swiss-Prot + TrEMBL  22-29




 Pairwise alignment  32-59  16-30
o Getting familiar with dot plots  32-28  16-19
o Studying influence word size on dot plots  39-40  20-21
o Read a dot plot  41-42  22-23
o Exploring the NW and SW algorithms  43  24
o Selecting the proper alignment tool  44-51  24-25
 52-59  26-30
o Effect of parameters on pairwise alignments
(gap opening penalty, the gap extension
penalty and the score matrix)


 60-66  31-34
 61-62  31-33
 Multiple alignment
o Progressive versus iterative methods
Differences between Clustal Omega, T-Coffee,
 63-66  34
MUSCLE and MAFFT
o Comparison of orthologous gene products
P2: Search and  Sequence similarity search  5-36  3-20
motifs o Reason & BLAST explained  6-10
o word size  18-19  3-5
o BLAST  20-36  5-20
Expected ( E ) value, UniProtKB/SwissProt, algorithm
parameters; MEGABLAST, BLASTx (proteins)

 39-56  21-29
 Sequence motifs  21-26
o Basic motif exercises  39-51
 ENSMBL
 Prosite
A curated and annotated protein
functional profiles and patterns database
 Interpro
Intergrates several sequence signature
databases such as Prosite, Pfam, Blocks,
ProDom and PRINTS.