Alignments

... want to design some primers to do some PCRs with. Nothing has been done about the genetics of the bird that I worked with so, I made some multiple alignments with the aa sequences of other organisms and found some well conserved regions that may serve as good start. However, I'm stuck about how ...

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think about what a sequence alignment is... in terms of looking for ORF's, you would probably use a tool like Expasy for that, sequence alignments serve a different purpose. Assuming line 1 and 3 are continuous, as are 2 and 4, what do they tell you? what does asterisk signify, do you think. ...

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... if there was a new tool that gave identical results and was twice as fast? ⋅ Are you happy with BLAST but just want to do much bigger alignments? Stuff like "Here's my 1M nucleotide sequence, give me the top 1000 local alignments", and get an answer in 10 seconds? ⋅ Or ...

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... using PFTOOLs (generalized HMMs) for nucleotide sequence motifs? While the original publication states, that the program is able to use DNA/RNA alignments for creating profile files, I do not see any option to build a profile out of a non amino acid alignment. (I know, that I could use the 6ft ...

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... the server will grind through an automated alogrithm for generating what ExPASY deems is the best overall structural alignment using your sequence alignments and any known structures. The nice part is that you don’t have to do very much. The downside is that neither do you have much control over ...

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