Programming Ideas

Ideas for Python coding:
– put sequences in fasta format

– parses sequences from fasta format

– reverse translate amino acid sequence

– search fasta file with EST for ORF

– search ncbi and pull fasta files for taxonomic groups and specific genes

– primer melting temperature
– GC content
– molarity calculations, e.g. http://www.graphpad.com/quickcalcs/molarityform.cfm

– SOMETHING FUNCTIONAL: blast2go
– upload a list of accessions
– enrichment analysis to get a chart of significant functional groups from a list of accessions

These require aligning:
– primer alignments to source sequences
– multiple alignments

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About Lisa Johnson

PhD candidate at UC Davis.
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