User: abhijit.synl

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abhijit.synl30
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Posts by abhijit.synl

<prev • 6 results • page 1 of 1 • next >
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Genome repeat masking before gene annotation
... Hello All, I wanted to know whether repeatmasking a genome or genome fragment, before performing gene annotation, is a good idea. The literature (http://www.nature.com/nrg/journal/v1...l/nrg3174.html, http://onlinelibrary.wiley.com/doi/1...eva.12178/full) and software such as MAKER, and PASA advoca ...
genome annotation bioinformatics written 9 days ago by abhijit.synl30
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BAC annotation strategy
... Hello All, I have a strategy question related to BAC annotation. I have 500 BAC sequences from a single maize line to annotate. I am faced with a strategy dilemma. 1) Put all the BAC sequences in one file, create a multi-fasta file and run the annotation. 2) Go about the annotation on a per BAC ...
sequence annotation bac written 8 months ago by abhijit.synl30 • updated 8 months ago by WouterDeCoster21k
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Getting plant full length cDNA sequences from NCBI
... Hello, I wanted to know if there was a method to download plant full length cDNA sequences from NCBI on a periodic basis. Lets say once every month. The way I am doing now is typing FLI_CDNA OR full-length OR "full length" in the search textbox, going to the Nucleotide section and selecting plant an ...
ncbi cdna update blast written 8 months ago by abhijit.synl30 • updated 8 months ago by apa@stowers320
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Comment: C: Getting the protein Domain architecture from a domtblout
... Thanks for writing the script Andrzej. It works!! I added the following two lines at the beginning of your code. Hope thats ok. # Parser for domtblout # Written By: Andrzej Zielezinski (http://www.staff.amu.edu.pl/~andrzejz/) From the code it appears that you wrote the script for hmmscan. Can it b ...
written 2.5 years ago by abhijit.synl30
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Answer: A: Getting the protein Domain architecture from a domtblout
... I'd like a tab-delimited output, something like Protein_ID<tab>Domain_Name<tab>Domain_ID<tab>Coordinates (for example 10..35) Other variations of output are also fine. Because I can write scripts to parse that out. I'd like to use the best e-val for domain presence/absence decis ...
written 2.5 years ago by abhijit.synl30
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Getting the protein Domain architecture from a domtblout
... Hello Everyone I have a million protein sequences that I ran against Pfam and now I have the corresponding domtblout files. I would like to get the summary architectures for each of these proteins. Someone has written a script in Bioperl, but I cannot get it to work. Is there a non-bioperl method o ...
sequence alignment written 2.5 years ago by abhijit.synl30 • updated 2.5 years ago by a.zielezinski7.3k

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Getting the protein Domain architecture from a domtblout

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