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Alternative procedure for generating FASTA sequences

Page history last edited by PBworks 13 years, 7 months ago

 

Alternative Method

by Ann Turner

 

Since I don't have access to the personal results pages, where the mutations are highlighted in red, I use the sequence at MitoMap.

 

For HVR1, I copy and paste the lines beginning with 16021 into a text editor.

(Very, very few HVR1 sequences will have mutations prior to 16024, which is where the "classical" HVR1 range begins.)

 

Then I use the numbers at the beginning of each line and count off the blocks of 10. For my mutation at 16293G I go to the line starting with 16261 and mumble to myself 16261-16271-16281-16291 to get to the block that would contain 16293. Then I count 16291-16292-16293 and replace the letter there (which happens to be an "a") with an upper-case G. The case does not matter at BLAST, so the upper case letter is sort of a flag for me.

 

The lines below also have my mutation at 16519C.

 

16021 ctgttctttc atggggaagc agatttgggt accacccaag tattgactca cccatcaaca

16081 accgctatgt atttcgtaca ttactgccag ccaccatgaa tattgtacgg taccataaat

16141 acttgaccac ctgtagtaca taaaaaccca atccacatca aaaccccctc cccatgctta

16201 caagcaagta cagcaatcaa ccctcaacta tcacacatca actgcaactc caaagccacc

16261 cctcacccac taggatacca acaaacctac ccGcccttaa cagtacatag tacataaagc

16321 catttaccgt acatagcaca ttacagtcaa atcccttctc gtccccatgg atgacccccc

16381 tcagataggg gtcccttgac caccatcctc cgtgaaatca atatcccgca caagagtgct

16441 actctcctcg ctccgggccc ataacacttg ggggtagcta aagtgaactg tatccgacat

16501 ctggttccta cttcagggCc ataaagccta aatagcccac acgttcccct taaataagac

16561 atcacgatg

 

Then I copy-and-paste those lines (with no further editing to remove numbers and spaces) into the box at BLAST.

 

Searching GenBank for mtDNA Sequences

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