User: horsedog

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horsedog20
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Posts by horsedog

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Maximum number of efetch
... Hi Pierre, is it possible to just get the fasta file instead of XML file? And I have no idea where to add retmax or retstart, this is my code: from Bio import Entrez Entrez.email = "A.N.Other@example.com" blast = open("file.txt").read() handle = Entrez.efetch(db="protein", id= blast, rettype="fasta" ...
written 23 days ago by horsedog20
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Maximum number of efetch
... Hi, I'm retrieving protein sequences from UID using efetch. I got more than 30000 UID but after running python script, it only gave me exact 10000 sequences, I'm wondering is there any limitation of number of retrieving, like 10000? Is it possible to get more 30000 at one time? Thanks ...
edirect written 24 days ago by horsedog20 • updated 24 days ago by Pierre Lindenbaum101k
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Comment: C: Define sequences length when doing blastx
... Not yet , now I'm studying evolution of a new gene in bacteria. I'm trying to find out the distribution of this gene in bacteria, the first step is to get the refseq nucleotide sequences of this gene, but only 58 genomes were found , I've done this, so now I'm trying to do blast in protein database ...
written 26 days ago by horsedog20
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Comment: C: Define sequences length when doing blastx
... Thanks for reply Michael, Yes you're correct, I thought about that before but since here I'd like to find as many species as possible, So I want to start from low value first and see how's going and then search more stringently. Here I set this cut-off from 300 to 500 is because I found this protei ...
written 26 days ago by horsedog20
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Define sequences length when doing blastx
... Hi, I'd like to use my nucleotide sequences to do the blastx to get protein sequences. Here is my command: *blastx -db refseq_protein -query outputA.fasta -out blastx.fasta -evalue 0.001* And I got more than 40000 results, which is too much, so I want to do some cut-off by defining length, for ex ...
blast written 26 days ago by horsedog20 • updated 26 days ago by Michael Dondrup43k
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Comment: C: Refseq accession number for protein and nucleotides
... So like for WP_069981055.1, which is protein electron transporter RnfB from *Geosporobacter ferrireducens* , but how can we know that where does it translated from? I just search the name *Geosporobacter ferrireducens* in gene database and it gives me two refseq number for genomes, one is NZ_CP0172 ...
written 27 days ago by horsedog20
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Refseq accession number for protein and nucleotides
... Hi, I have a basic question about the accession number in reference sequence. For non-redundant protein is WP_ and for nucleotides is NZ_. Here I got thousands of protein sequence with different accession number. My goal is to find out if certain proteins are from the same genome, which means if som ...
ncbi written 27 days ago by horsedog20 • updated 26 days ago by Jean-Karim Heriche13k
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Extract the targeted txt using python
... Hi, I'm beginner to python, here I have a very basic question about extracting targeted text. I have thousands of strings like this : >ref|WP_070076791.1| iron-sulfur protein [Acinetobacter proteolyticus] Here I only need WP_070076791.1, so I write a script in python: data = open("data ...
python written 28 days ago by horsedog20 • updated 28 days ago by WouterDeCoster23k
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Use NCBI WP_ non-redundant protein to find out the genome accession number
... Hi, I'm doing blastx using nucleotides aligned sequences to find out similar non-redundant protein sequence . Here I have a question, I want to know that if the proteins that are found out are from the same genome or not, which means if they share the same accession number. Is it possible to do tha ...
blast written 29 days ago by horsedog20
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FastTree running problem
... Hi all, I'm using FastTree Version 2.1.10 SSE3 to do the phylogenetic analysis. But here I ran into a problem, it keeps giving me the error : Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN clos ...
software error written 5 weeks ago by horsedog20 • updated 4 weeks ago by h.mon9.2k

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