Java Equivalent Of Biopython'S Ncbixml Parser

I'm looking for a method similar to Biopython's parse method of NCBIXML in java

this is the parse method http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-module.html#parse

java blast xml biojava biopython parser python

• 2,461 views • link

updated 13.1 years ago by David W

• written 13.1 years ago by aliahmadvand2004 •

1 answer

BioJava is probably the first place to try.

I have no experience with it, but the wiki has a page on parsing BLAST XML

• 72 views • link

written 13.1 years ago by David W

More posts like this

How can I run a Biopython qblast search targeting a specific set of organisms?
written 6.2 years ago by sviatoslav.kendall

I want to use Biopython's qblast() command to query NCBI's databases but I want to limit my search to specific organisms. Looking at the [documentation …
Biopython NCBIXML Parsing - Field Parameter
written 8.5 years ago by maximilian.mayerhofer •

Hey, I want to extract the <Iteration_query-def> from my blast Output (outfmt 5). According to the source code ( http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-pysrc.html) it should be something like …
AttributeError: 'Hit' object has no attribute 'sacc_ver'
written 8.8 years ago by bioinfoSeeker •

Hi, I am trying to write a script to parse and summarize the ncbi web blast output (14 columns). I am using biopython searchIO on …
how to parse XML blast output
written 9.8 years ago by Farbod

Hello everyone, (I am not native in English) I want to parse **XML** local blast result (transcripts against NCBI nr) to see the name of …
Documentation about Bio. Site.search_pwm method in BioPython
written 10.1 years ago by Rox

Hi everyone, It's my first time with biopython, and I want to use a method described in a paper I'm interested in ( Emily Clough …
amino acid weight confusion
written 11.8 years ago by jsbrava •

I'm taking a class that uses stepic.org. We're given a list of amino acid weights: https://stepic.org/lesson/CS-Generating-the-Theoretical-Spectrum-of-a-Peptide-4912/step/1 For example, it gives the weight of A as …
How to convert a Generic Affymetrx CEL file to Biopython compatible CEL file?
written 12.2 years ago by towi •

I have a `*.CEL` file which is obviously in [generic CEL file format][1]. To handle it more easily I would like to read it with …
Update Biopython'S Seqrecords?
written 13.5 years ago by biocyberman

<p>I looked at the documentation here: <a href="http://biopython.org/wiki/SeqRecord">http://biopython.org/wiki/SeqRecord</a> , but I did not find any information or methods to update properties of SeqRecords. I want …
Invalid Api For Biopython'S Blast?
written 14.8 years ago by Jesse J

<p>According to <a href="http://biopython.org/DIST/docs/api/">BioPython's API</a>, Bio.Blast.NCBIWWW.qblast() should have a parameter of specifying megablast to be true or false. When I set my qblast as</p> <pre><code>result_handle …
How To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
written 15.9 years ago by Niek De Klein

<p>I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need …