User: mittjohns

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mittjohns30
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United States
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7 months, 2 weeks ago
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4 years, 10 months ago
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m********@gmail.com

Posts by mittjohns

<prev • 7 results • page 1 of 1 • next >
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Comment: C: cut a fasta file into two columns of pos and single base
... thanks Pierre, a brilliant use of grep -o and cat -n. ...
written 7 months ago by mittjohns30
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cut a fasta file into two columns of pos and single base
... What’s the most efficient (fast and simple code) way to convert/cut a fasta file (either part or the whole sequence) of a chromosome into two column tab-delimited format of pos and base? For example: #fasta file \>chr2 ATGCATTC... #converted pos-base file 1 A 2 T 3 G 4 C … I know w ...
fasta base sequence position written 7 months ago by mittjohns30 • updated 7 months ago by Pierre Lindenbaum124k
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Comment: C: Map genetic mutations to protein domain/structure
... Thank you for all the info. I tried the MutDB. It requires identifiers for the mutations (dbSNP etc). most time, we only have the genomic positions and nucleotide substitutions. Hence it doesn’t work. It is easy to locate the InterPro file to download, but not the ones in NCBI's CDD. Which file(s) ...
written 4.9 years ago by mittjohns30
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Answer: A: Map genetic mutations to protein domain/structure
... Try to bring this up so that people can still see it… ...
written 4.9 years ago by mittjohns30
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Comment: C: Map genetic mutations to protein domain/structure
... Thank you Sam. You mean, Uniprot provides protein domain data. Is their data more comprehensive or better than data from Pfam or PDB? BTW, where is their domain data available for download? ...
written 4.9 years ago by mittjohns30
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Comment: C: Map genetic mutations to protein domain/structure
... Just want to clarify, I don’t need to predict effect of the mutation on the protein structure (i.e. potential structure changes etc). I just need to map and visualize the mutation on the known 3D structure of the native protein (with the affected residues labelled). This may reveal whether/how that ...
written 4.9 years ago by mittjohns30
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Map genetic mutations to protein domain/structure
... I am trying to map genetic mutations to protein domain/structure. Ideally, I want to visualize the variants in linear protein domain diagram and 3D protein structure like the attached images. I did research, but I can’t find good tools/databases for such work. I know similar questions have been ask ...
domain mutation protein structure written 4.9 years ago by mittjohns30 • updated 3.5 years ago by Collin680

Latest awards to mittjohns

Great Question 4.9 years ago, created a question with more than 5,000 views. For Map genetic mutations to protein domain/structure
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Map genetic mutations to protein domain/structure
Student 4.9 years ago, asked a question with at least 3 up-votes. For Map genetic mutations to protein domain/structure

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