Hello Everyone!
If someone wouldn't mind helping me along here I would really appreciate it...
I have a bunch of sequences from different species. I've been able to identify (using BLAST) a few of them, but there are many that are unknown (no strong BLAST matches) They were all amplified with the same primer pair, but have produced amplicons of different sizes. They don't align unless there are a million (or so it seems) gaps. Some of the sequences are so divergent they don't align at all!
I would eventually like to draw a tree to give insight into where an unidentified sequence belongs.
Do all those gaps affect how the tree will be constructed? What do I do about the sequences that I can't align with the others??
Is there a book that might help me out with this?
Any advice I can get would be great.
Thanks,
Kirsten
If someone wouldn't mind helping me along here I would really appreciate it...
I have a bunch of sequences from different species. I've been able to identify (using BLAST) a few of them, but there are many that are unknown (no strong BLAST matches) They were all amplified with the same primer pair, but have produced amplicons of different sizes. They don't align unless there are a million (or so it seems) gaps. Some of the sequences are so divergent they don't align at all!
I would eventually like to draw a tree to give insight into where an unidentified sequence belongs.
Do all those gaps affect how the tree will be constructed? What do I do about the sequences that I can't align with the others??
Is there a book that might help me out with this?
Any advice I can get would be great.
Thanks,
Kirsten
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