Difference between revisions of "CSC334 Lab1"
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In this lab we retrieve a DNA sequence in FASTA format that we can use for various experiments. | In this lab we retrieve a DNA sequence in FASTA format that we can use for various experiments. | ||
| + | ==Procedure== | ||
* Point your browser to [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed www.ncbi.nlm.nih.gov] | * Point your browser to [http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed www.ncbi.nlm.nih.gov] | ||
* Select Nucleotide from the drop-down menu, and enter escherichia coli in the search box. | * Select Nucleotide from the drop-down menu, and enter escherichia coli in the search box. | ||
| Line 56: | Line 57: | ||
* That's it, you have your first [http://en.wikipedia.org/wiki/FASTA FASTA] sequence for a nucleotide of the E. Coli bacteria. You can store it in a text file or copy and paste it in a program or a Web form, depending on what you want to do with it. | * That's it, you have your first [http://en.wikipedia.org/wiki/FASTA FASTA] sequence for a nucleotide of the E. Coli bacteria. You can store it in a text file or copy and paste it in a program or a Web form, depending on what you want to do with it. | ||
| + | |||
| + | ==References/Misc. Links== | ||
| + | |||
| + | <hr> | ||
| + | © D. Thiebaut 2008 | ||
Revision as of 16:39, 21 July 2008
Retrieving a Nucleotide (DNA) sequence from the NCBI database
In this lab we retrieve a DNA sequence in FASTA format that we can use for various experiments.
Procedure
- Point your browser to www.ncbi.nlm.nih.gov
- Select Nucleotide from the drop-down menu, and enter escherichia coli in the search box.
- Click on the first link, in our case on AB426820, and select FASTA in the display box. You should get something like this (note that the first line may wraps around, and should not include a carriage return):
>gi|194306025|dbj|AB426820.1| Escherichia coli ompT mRNA for outer membrane protease T, partial cds, strain: JCM 5491 TGGGAATAGTCCTGACAACCCCTATTGCGATCAGCTCTTTTGCTTCTACCGAGACTTTATCGTTTACTCC TGACAACATAAATGCGGACATTAGTCTTGGAACTCTGAGCGGAAAAACAAAAGAGCGTGTTTATCTAGCC GAAGAAGGAGGCCGAAAGGTCAGTCAACTTGACTGGAAATTCAATAACGCTGCAATTATTAAAGGTGCAA TTAATTGGGATTTGATGCCCCAGATATCTATCGGGGCTGCTGGCTGGACAACTCTCGGTAGCCGAGGTGG CAATATGGTCGATCGGGACTGGATGGATTCCAGTAACCCCGGAACCTGGACGGATGAAAGTAGACACCCT GATACACAACTCAATTATGCCAACGAATTTGATCTGAATATCAGAGGCTGGCTCCCCAACGAACCCAATT ACCGCCTGGGACTCATGGCCGGATATCAGGAAAGCCGTTATAGCTTTACAGCCAGAGGGGGTTCCTATAT CTACAGTTCTGAGGAGGGATTCAGAGATGATATCGGCTCCTTCCCGAATGGAGAAAGAGCAATCGGCTAC AAACAACGTTTTAAAATGCCCTACATTGGCTTGACTGGAAGTTATCGTTATGAAGATTTTGAGCTAGGTG GTACATTTAAATACAGCGGCTGGGTGGAAGCATTTGATAACGATGAACACTATGACCCAGGAAAAAGAAT CACTTATCGCAGTAAAGTCAAAGACCAAAATTACTATTCTGTTGCAGTCAATGCAGGTTATTACGTAACG CCTAATGCAAAAGTTTATATTGAAGGCGCATGGAATCGGGTTACGAATAAAAAAGGTGATACTTCACTTT ATGATCACAATGATAACACTTCTGACTACAGCAAAAATGGTGCAGGCATAGAAAACTATAACTTCATCAC TACTGCTGGTC
- That's it, you have your first FASTA sequence for a nucleotide of the E. Coli bacteria. You can store it in a text file or copy and paste it in a program or a Web form, depending on what you want to do with it.
References/Misc. Links
© D. Thiebaut 2008
