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.
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.
