DNA
and protein sequence retrieval and homology searches
NCBI/Entrez
(sequence retrieval/Genbank)
NCBI BLAST (search for
homology in sequence databases)
things slow on this side of the Atlantic? Try EMBL...
SRS
(Sequence
Retrieval System/EMBL)
EMBL BLAST(search
for homology in sequence databases)
sequence
manipulation
BCM Search Launcher
(translation, reverse complement, alignment..etc)
gene
structure
NetPlantGene (predict
splice sites)
RepeatMasker
(repeat detection in genomic sequence)
ORF finder (search
for open reading frames in DNA sequence)
WebGene (prediction of
gene structure, TATA boxes, poly-A sites and splice sites)
Internet Resources
for UTR analysis (databases of UTR sequence and search tools for detecting
UTR functional elements)
promoter
detection and analysis
PLACE
or PlantCARE
(search for known plant cis-acting elements)
PROSCAN (detection
of Eukaryotic promoter regions in genomic DNA)
Improbizer
, MEME , AlignAce
(novel motif detection using multiple sequences)
MotifMatcher
(find a known motif in a sequence)
MAST
(search for a motif in a database, uses MEME output format)
genomics
Glimmer
(gene finder for Arabidopsis and rice genomic sequence; TIGR)
Other
TIGR genomics tools
GenomePixelizer
(a comparative genomics tool that allows you to illustrate relative gene
positions on chromosomes)
Nature's
Genome Gateway (includes a list of all genomics papers in Nature
and Nature Genetics and links)
protein
analysis
ExPASy(proteomics
tools including protein identification and characterization, 1', 2', 3'
structure analysis, postranslational modification prediction)
FSSP
database (find structural neighbours of a protein already in the Protein
Data Bank)
online
sequence alignment (www) and free software (s)
-
ClustalW alignment www
(global* sequence alignment, and treefile creation)
-
ClustalW, MSA, ctreewww
(three different alignment programs)
-
ToPLign www (global,
free shift* and local* alignments with multiple visualization modes)
-
BLAST-2 www
(local alignment of two sequences)
-
ClustalW
with JalView www (Jalview multiple sequence editor, has some
neat analysis features)
-
BOXSHADEwww
(preparing pre-aligned sequences for publication)
-
TreeViews
(for
viewing and editing treefiles, compliments of the University of Glasgow
)
-
Divide and
Conquer (free shift alignments)
*Free shift
alignments will ignore gaps at the beginning and end of the sequence, while
Global
alignments try to consider all positions. Use Free shift alignments when
some of the sequences are terminally truncated.
Local
alignments (such as BLAST) are useful for finding short stretches of homology
and are useful for finding sequence overlap or detecting a short internal
sequence stretches that are shared.
Specialty Sites for Plant Molecular Biologists
PPMdb
(Arabidopsis plasma membrane proteins: includes 2-D, expression,
and sequence data)
PLMItRNA
(database for tRNA molecules and genes in mitochondria of photosynthetic
eukaryotes)
PEDANT
(a complete chromosome by chromosome catalog of Arabidopsis ORFs
with associated analysis such as BLAST matches, molecular weight etc.)
PCR
Codon Usage
Gene Databases:
TIGR databases
People | Research Areas
| Department of Plant Agriculture |flashlinks
BeanGenes
(Phaseolus, Vigna spp.)
Soybase
(Glycine max)
MaizeDB
(Zea maize)
BrassicaDB
(Brassica napus)
SolGenes
(Lycopersicon, Solanum etc.)
AtDB
(TAIR) (Arabidopsis thaliana)