Finding Genes in a 1500 Nucleotide DNA Sequence - Results

Sequence

• Three DNA sequences
• Sequences aligned
• 1500 nt sequence stretch
• 1500 nt sequence full clone
• 1500 nt sequence in FASTA format
• Conclusion

Worksheet

• Gene-finding worksheet
• Instructions

Sequence Statistics (Is sequence biological or random?)

• Sequence statistics a
• Sequence statistics b
• Sequence statistics c
• Sequence statistics d
• Sequence statistics e
• Sequence statistics f
• Conclusion

Promoter Predictions (Where might gene start?)

• Core Promoter transcriptional start site predictions cover page
• Core Promoter transcriptional start site predictions input "Watson"
• Core Promoter transcriptional start site predictions results "Watson"
• Core Promoter transcriptional start site predictions input "Crick"
• Core Promoter transcriptional start site predictions results "Crick"
• Berkeley promoter predictions input
• Berkeley promoter predictions results
• CBSA promoter predictions input
• CBSA promoter predictions results
• CpG promoter predictions input
• CpG promoter predictions results
• McPromoter promoter predictions input
• McPromoter promoter predictions notification
• McPromoter promoter predictions result
• Conclusion

Poly-A Signal Predictions (Where might gene end?)

• Polyadq poly-A signal sequence predictions input "Watson"
• Polyadq poly-A signal sequence predictions result "Watson"
• Polyadq poly-A signal sequence predictions input "Crick"
• Polyadq poly-A signal sequence predictions result "Crick"
• Conclusion

Splice Site Predictions (Where might exons and introns be?)

• Berkeley splice site predictions input a
• Berkeley splice site predictions results a
• Berkeley splice site predictions input b
• Berkeley splice site predictions results b
• Conclusion

ORF's and Translations (Which exons and introns might be real?)

• NCBI open reading frames input
• NCBI open reading frames 100-nucleotide setting
• NCBI open reading frames 50-nucleotides setting
• NCBI open reading frames ORF 593-928
• NCBI open reading frames Starts-and-Stops view
• BCM 6-Frame translation a
• BCM 6-Frame translation b
• BCM 6-Frame translation c
• BCM 6-Frame translation d
• BCM 6-Frame translation e
• BCM 6-Frame translation f
• Conclusion

TATA-Box Predictions (Does the promoter for this gene contain a TATA-Box consensus sequence? Where is it located?)

• ICG TATA-Box predictions input 1,500
• ICG TATA-Box predictions result 1,500
• ICG TATA-Box predictions input 400
• ICG TATA-Box predictions output 400
• Conclusion

Messenger RNA Evidence (How could mRNA evidence, such as Expressed Sequence Tags -ESTs- and full-length cDNA aid in gene prediction?)

• Messenger RNA sequences
• Alignment of genomic sequence with full-length messenger
• Alignment of genomic sequence with EST clone 1
• Alignment of genomic sequence with EST clone 2
• Conclusion

Gene Prediction Programs (Where would gene prediction programs find a gene in this sequence?)

• Genscan gene prediction page
• Genscan gene prediction input
• Genscan gene prediction result
• Genscan gene prediction result graphic
• Grail gene prediction page
• Grail gene prediction input
• Grail gene prediction intermediate
• Grail gene prediction result
• HMM gene prediction input
• HMM gene prediction result
• FgenesH gene prediction input
• FgenesH gene prediction result
• Conclusion

Gene in GenBank (What could the gene be? Are there other sequences like it in the databases?)

• Go to NCBI Blast search, option a
• Go to NCBI Blast search, option b
• NCBI Blast search options
• NCBI Blast search input
• NCBI Blast search process
• NCBI Blast search results
• Genbank entry 900 nucleotides
• Genbank entry 1,704 nucleotides
• Genbank entry for human alpha globin region; 43058 nucleotides
• Conclusion

Gene in Genome (Where exactly is the gene located in the human genome?)

• Go to NCBI Map Viewer, option a
• Go to NCBI Map Viewer, option b
• NCBI Genome Viewer
• NCBI genome Blast 1
• NCBI genome Blast 2
• NCBI genome Blast result
• NCBI genome result view
• NCBI chromosome view 1
• NCBI chromosome view 2
• NCBI chromosome view 3
• NCBI chromosome view 4
• NCBI chromosome view 5
• NCBI chromosome view 6
• NCBI chromosome view 7
• NCBI show sequence
• NCBI sequence view
• Conclusion

Summary

• Results summary