2. Plant DNA Barcoding: data workflow
Workflow Outline:
raw sequence editing
data alignment
re-edit the sequence file
upload to BOLD
quality checks using BOLD / genbank
9. Sequence Alignment
After editing: need to align the data
Kelchner (2000) Ann Missouri Bot
Gard
rbcL easy to align - most programs work well
matK tricky to align – TransAlign seems to do the
best job
trnH difficult (impossible between genera?)
ITS difficult (impossible between genera?)
Clustal www.clustal.org
TransAlign http://www.biomedcentral.com/1471-2105/6/156
K-Align http://www.ebi.ac.uk/Tools/msa/kalign/
10. Sequence Alignment
Problems to look for after alignment:
- primers not trimmed
- gaps at the ends
- gaps in the middle (protein coding)
- translation shows stop codons
11. - primers not trimmed trnH-psbA
- gaps at the ends Real data submitted for
publication
12. rbcL
- gaps in the middle of a data submitted for publication
coding region