New answers tagged bioinformatics
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In order:
Unfortunately, there's no easy way to batch query with only location. You could look up SNPs within genes here. (You could find the gene a SNP is located in by searching an annotated human genome file for the position.)
You can figure out whether it's in 3'UTR by comparing to a list of human 3' UTRs. The UCSC genome browser page here will help: ...
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Here is a good overview of primer design considerations when using Gibson assembly.
http://j5.jbei.org/j5manual/pages/22.html
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You can take a look at this tutorial to understand TCGA MAF files. And you can find a list of TCGA MAF files containing mutations mapped to genes and miRNA at https://www.synapse.org/#!Search:syn1710680
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If you're looking for an exact match, you don't really need a complex aligner. Perl regular expressions are pretty powerful at string transformations or conditional matching of substrings. For example, to find all matches of AASYWSRA in a nucleotide sequence $seq, you can do:
@matches = $seq =~ m/AA[CG][CT][AT][CG][AG]A/g;
The [] brackets are known as ...
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Disclaimer: I haven't ever done a Gibson assembly, but here is my theoretical understanding of how to design your primers. You need four 40mers each consisting of 20 bp segments derived from the vector and the insert and corresponding to the junctions that you are trying to create. In the diagram below the dotted lines represent the junctions between the two ...
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Well SNPs are single nucleotide polymorphisms. Some SNPs are in the coding regions of genes and they can result in changes in the resulting protein. For example, the SNP rs1801131 is a human variation where some individuals have a G instead of an A at position 1515 of the gene MTHFR. When the gene is transcribed and then translated into protein, this ...
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At the MEME server page, there's a link to upload a customized background markov model (using the command line interface, this is the -bfile option). From there, there's a link to the MEME Man Page. Under "Objective Function", it specifies:
The background model is an n-order Markov model. By default, it is a 0-order model consisting of the ...
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You can use "as" to switch to a particular style (http://pymolwiki.org/index.php/As
):
as cartooon, 11AS and chain a
You can also hide everything, to remove all representations (http://pymolwiki.org/index.php/Hide):
hide every, 11AS and not (n. ca+c+n and resi 5-10)
I'm a fairly expert user of PyMOL and I've never seen an API exposed which will show ...
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Just to flesh out Daniel Standage's answer a bit, remember that a genome is double stranded with one strand being complementary to the other. Genes can be found on either strand, the two are equivalent biologically. However, sequencing projects choose one of the two strands (randomly) and call it the plus (+) strand and then save all sequences with respect ...
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Note that the query sequence you have provided matches the minus strand of your target sequence. That means not only that the target sequence will be reversed (as you have noted), but it will also be complemented as well. So in the GenBank record, you should not look for the sequence CCGACCGA... starting at position 10835, you should look for the sequence ...
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What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
If I understand what you're attempting to accomplish, as David said, this is a vigorous area of study in structural biology. I'll start by saying that a single amino acid substitution will often make virtually no difference in a structure, but there are proteins where a couple substitutions will convert an all alpha-helical protein to all beta-sheet, so I'll ...
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I'm resurecting an old question, but I've heard this question from a few young bioinformaticians and had a couple more points to consider about compressing PDB files.
The first is that many PDB files (including all PDBs hosted on the PDB site) have some 300-400 lines of meta data at the top of the file. This accounts for about 10-20% of the total file ...
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I'd tend to agree there's very little data on this, esp given how many isoforms there are. I believe that even some cases of pseudogenes may have function as a protein. I'd bet that most of them have some unique functional aspects.
I think we'd all agree we can't prove that they do in all cases, but let me sketch out how these different functions might ...
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It seems that most functional annotation these days is inferred from sequence similarity to previously annotated genes/proteins: this is certainly true of high-throughput functional annotation. It's hard to know how many layers of inference there are between your query sequence and an actual experiment verifying the (possibly tissue- or condition-specific) ...
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I've never utilized the feature, but I know Vmatch allows you to define your own alphabets and symbol mappings, which should allow you to handle the IUPAC ambiguous nucleotide symbols. The default alphabet/mapping may even include these symbols.
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