User: marlenejensen

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Posts by marlenejensen

<prev • 10 results • page 1 of 1 • next >
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Database annotation for metaproteomics
... Hey all, I am using a metaproteomic database for the gut microbiome of mice which I found online http://gigadb.org/dataset/view/id/100114/token/mZlMYJIF04LshpgP. Unfortunately, the accession numbers and protein descriptions are not really helpful for taxonomic analyses since they are like this: ...
next-gen written 16 days ago by marlenejensen20 • updated 16 days ago by RamRS21k
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Comment: C: What is the best/most accurate protein secretion signal predictor?
... Yes, right....I forgot that. I have bacteria sequences and want to look at pathway IV.. ...
written 3 months ago by marlenejensen20
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What is the best/most accurate protein secretion signal predictor?
... Hey, can you recommend a good protein secretion predictor? I am running SignalP, TatP,SecretomeP, Phobia and PrediSi but the results differ a lot. Do you have some experience with that? Thanks a lot in advance! ...
predictor sequence written 3 months ago by marlenejensen20 • updated 3 months ago by finswimmer11k
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Comment: A: How to extract pattern matching sequences from a fasta file?
... Finally fixed it. Thank your for your support guys! ...
written 3 months ago by marlenejensen20
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Comment: C: How to extract pattern matching sequences from a fasta file?
... When I tried to use that I got this error. Error: Could not find or load main class Lab.Data.current. Caused by: java.lang.ClassNotFoundException: Lab.Data.current. I am super sorry for all the confusion...I just started with all this and I am still struggling a lot. I think I forgot to say that I ...
written 3 months ago by marlenejensen20
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Comment: C: How to extract pattern matching sequences from a fasta file?
... samtools faidx OlaviusV10.fasta Delta1 [E::fai_build_core] Different line length in sequence 'Symbionts_6frame_scaffold_2458_1' Could not load fai index of OlaviusV10.fasta ...
written 3 months ago by marlenejensen20 • updated 3 months ago by finswimmer11k
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Comment: C: How to extract pattern matching sequences from a fasta file?
... Yes I tried to run the command but then I got the errror that there is one sequence with a differnet line length which is why it cannot work. So I was thinking that I maybe need to normalize my file? ...
written 3 months ago by marlenejensen20
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Comment: C: How to extract pattern matching sequences from a fasta file?
... Thank you! I tried this bit there is a different line length in one of the sequences...is there an option to ignore that case? ...
written 3 months ago by marlenejensen20
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Comment: C: How to extract pattern matching sequences from a fasta file?
... It has folded sequences with multiple lines....is it possible to take that into account? ...
written 3 months ago by marlenejensen20
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How to extract pattern matching sequences from a fasta file?
... Hi :) I have a huge fasta file containing sequences from several organisms (endosymbiosis) and I want to extract the sequences for each organism respectively. Since my scripting skills are very, very basic I was wondering if there is way to do this in my ubuntu command line without a script? Of cou ...
sequencing written 3 months ago by marlenejensen20

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