ChromDB Help File

Help Manual Contents

I. Search Functions
A. Quick Search Text Box
1. Gene name or synonym (alias)
2. Locus
3. Organism

B. Advanced Search for Information Retrieval

1. Step 1: Starting the process
a. Option 1: Search by a list of gene/protein names
b. Option 2: Search by taxon criteria using pre-set groups of organisms
c. Option 3: Customize your organism selection from a list
2. Step 2: Selection of protein classifications
a. Option 1: Selection using functional groupings
b. Option 2: Alphabetical listing of protein groups
3. Step 3: Select the type of reports or displays
C. BLAST programs at ChromDB
II. Report Utilities
A. ChromDB Contents
1. Option 1: View all proteins
2. Option 2: View proteins of functionally related proteins
3. Display output
4. Organism filter

B. Sequence Tools

1. FASTA file format for protein, transcript, or genomic sequences
a. Generate FASTA format files for a list of gene/protein names.
b. Generate FASTA format files using pre-set groups of organisms.
c. Generate FASTA format files using “Select an organism” link in Step 1
d. Select protein classifications (Step 2)
e. Select the sequence type
2. FASTA file format for protein domains
C. Plant Genomes
1. Arabidopsis thaliana
2. Medicago truncatula
3. Orysa sativa ssp.japonica
4. Physcomitrella patens
5. Populus trichocarpa
6. Zea mays
D. Genomic-based Reports
1. Genomic-based versus transcript-based organisms
2. Genome-based tools
E. Protein Information
F. Gene Counts
G. Loci
H. Synonyms
III. Viewers
A. Exon View
B. Protein Domain View
IV. ChromDB Nomenclature
V. Gene Record Pages
A. General Information
B. Vector Information
C. Order Vectors
D. RNAi lines
VII. ChromDB Mission
VIII. Acknowledgements

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