Questions tagged [java]

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How does BioJava retrieve bond information from a PDB file?

How can I compute energy from a protein PDB file? I asked the above question. Then I thought, Why don't I check how BioJava obtains bond information from a protein PDB file? Surprisingly, BioJava's ...
user366312's user avatar
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Error while opening xmfa generated by progressiveMauve

I used commandline progressiveMauve to align two genome .gbk files. The alignment was successful. But when I try to visualize the final .xmfa file with Mauve, I get the following error. ...
venkatesh war's user avatar
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Print indel/mismatch in a blastp stream

I am in need of a simple tool that accepts an XML file generated by a BlastP as input and gives me back a file containing information about mismatches/indels/etc. Fortunately such a tool already ...
Eduardo M.'s user avatar
2 votes
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Drawing synteny using CIRCOS from progressive MAUVE alignment

I am using Mauve app to align two whole genomes. I've aligned these genomes (gbk files) with the progressive Mauve aligner, and I got sp.sslist, sp.xmfa, sp.guide_tree,sp.backbone file, sp.bbcols etc ...
Umar's user avatar
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java error when running CIRI-full.jar Merge module

I have an issue running a module trying to detect circRNA from RNAseq data. The error is a java error and I have not knowledge of java so I don't understand the issues and googling hasn't helped. the ...
Elhadi Iich's user avatar
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Java Protein Comparison Visualisation

I have project where I am required to build a visual analytics tool into an existing Java project to visually compare and analyse protein sequences from SwissProt, GenBank, EMBL etc. (downloaded from ...
user10169's user avatar
1 vote
2 answers

Mapping statistics from bam file using bbtools and sambamba

Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using from bbtools on bam files. It gives 77% mapped and 5% unmapped, what about the remaining 18% ...
bioinfonext's user avatar
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Java error when trying to run UBCG jar (java.lang.ClassNotFoundException)

I wanna install UBCG.JAR in ubuntu 18.04 but I cannot run the java File UBCG.JAR. when I type the code java -jar UBCG.JAR an error message appears. ...
Maloki's user avatar
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Is there a way to use BioLemmatizer from Python?

Lemmatization is one of the most important tasks for text normalization in natural language processing (NLP), i.e. using deep learning to understand text data. One of the good lemmatizers I found for ...
PinkBanter's user avatar
1 vote
2 answers

GSEA - Gene Set Enrichment Analysis - in R studio

I have been trying to conduct a classic GSEA using the broad institute software and can not figure out how to compile it in R for the life of me. I am aware that there exists other packages in R that ...
h3ab74's user avatar
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