User: kayrouz.1

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kayrouz.10
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Posts by kayrouz.1

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Comment: C: Batch Retrieval of Conserved Domains from a List of IDs?
... You have solved my problem, thank you! ...
written 5 months ago by kayrouz.10
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Batch Retrieval of Conserved Domains from a List of IDs?
... **Background:** I have a large number (>100,000) of functionally unrelated protein sequences and I want to generate a roughly functional annotation for each. I've tried PROKKA and RASTtk, but they tend to return a large number of "hypothetical" results so I've changed my approach. So far I have ...
ncbi entrez conserved domain written 5 months ago by kayrouz.10 • updated 5 months ago by vkkodali1.1k
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Grouping secondary metabolite gene clusters into families
... I have a set of ~1000 bacterial secondary metabolite gene clusters that all encode biosynthesis of the same class of compound, based on a couple marker genes common to all clusters. However, they also have variable regions which encode a wide variety of modifying enzymes. I have nucleotide fasta fil ...
gene cluster grouping clustering families written 13 months ago by kayrouz.10
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Batch Annotation of Bacterial Gene Clusters
... I have around 1000 nucleotide sequences, each of which represents a bacterial gene cluster. Each sequence is around 30kb in length and they come from many different genera (some are even metagenomic sequences). Is there a convenient way to accurately annotate these gene clusters in batch form and re ...
annotation gene cluster batch written 16 months ago by kayrouz.10
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How to extract variable nucleotide regions from a list of contigs
... I have a list of about 6000 NCBI contig accession numbers and I'd like to extract a specific 30kb region from each contig. I have, in a separate file, a list of "begin" and "end" indices that represent the region of interest for each contig. Is there a way to retrieve a fasta file of these trimmed c ...
extract contig refseq blast written 18 months ago by kayrouz.10 • updated 18 months ago by Vijay Lakhujani4.1k

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