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Tool to analyze the AT-content of all the genes from a database?

I am interested in finding the AT-content of all the genes of Saccharomyces cerevisiae(SC). Is there a tool available that can analyze the entire genome database of SC and can tabulate the genes in the order of their AT-content? Moreover, it would be great if the tool can analyze any fixed sequence length of each gene in the database, say, the first 100bp of all the genes and then tabulate them in the order of their AT-content?

sequence
• 2,013 views • link
updated by Ram Ram • written by merajrizvi.83 • merajrizvi.83

2 answers

  • Get the coordinates of your genes, as a BED, for example using the UCSC table browser.
  • Extend if needed, the sequences of the BED with bedtools slop
  • Download the sequence of your genome
  • Extract the base-content of the BED with bedtools nuc (see Calculating Gc Content For All Ccds)
• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

You can also do this with Galaxy tools.

Use a set of gene coordinates

Fetch Alignments/Sequences -> Extract Genomic DNA

Emboss -> geecee

• 1 views • link
updated by Ram Ram • written by jotan jotan

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