Online Tutorial for Sequence Alignment
& Analysis
Portal
for searching sequence similarities (FASTA, BLAST, Smith-Waterman), patterns, profiles, motifs (e.g., PROSITE), and for performing protein sequence analyses, protein secondary structure predictions and gene analysis/prediction.
*Alignment Presentation
Methods
Prosite
|
Prints
|
Blocks
|
Pfam
|
ProfileScan
|
eMotif
|
Resources for Identification of Protein-coding
Sequences
Program
|
Organisms |
CDSB |
nematode/yeast/plant/bacteria |
|
|
many species |
|
|
human |
|
|
human/Drosophila |
|
|
vertebrate/Caenorhabditis/maize/Arabidopsis |
|
|
human/mouse/diptera |
|
|
human |
|
|
any |
Resources for Repeat
Analyses
|
Program |
Organism |
|
CENSOR: annotates and masks repeats |
Human/rodent |
|
RepBase: repeat collection |
Human/several
others |
|
Repeat Masker: annotates and masks
repeats |
Several
subgroups of vertebrates |
|
*XBLAST: tools for masking repeats |
Any |
*ftp ncbi.nlm.nih.gov; pub/jmc
Databases Collections
Database
|
Category
|
KEGG
|
Metabolism
|
Metabolic
DB
|
Metabolism
|
WIT
|
Metabolism
|
Mito-Pick
|
Metabolism
|
ProNet
|
Protein-Protein Interactions
|
Protocols
|
Cell and Molecular Biological Methods
|
Protein SCI
|
Amino Acid Side-chain Interactions
|
GenomeNet
|
Genomes
|
MAGPIE
|
Genomes
|
|
Major programs for phylogenetic analyses: |
|
Tutorials: |
Resources for
Genome Biology On-line tutorials Some on-line databases: