User: weslfield

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weslfield90
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Posts by weslfield

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Bulk Download Of Ncbi Gene "Summary" Field
... We at SolveBio have also run into this problem while parsing these flat files. There are some odd exceptions and omissions in these flat files. For instance, sometimes records appear with no summary or there are duplicate records. There are even instances where the gene is just absent. Here is an ex ...
written 3.3 years ago by weslfield90
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Problems running local Blastp: No hits found when there should be
... Hi all, when I run the following command for a local Blastp, I get no results returned even though there should be results. blastp -out /Users/Wes/Desktop/new_pairwise/blast.xml -outfmt 5 -query /Users/Wes/Desktop/new_pairwise/gyra_ref.txt -db blastdb Here is the XML output from blastp: <?xml ...
alignment blast blastp written 4.6 years ago by weslfield90 • updated 4.6 years ago by Biostar ♦♦ 20
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Comment: C: Pairwise vs. Multiple Sequence Alignments: Which has better accuracy?
... These are sequences extracted from a metagenomic sample targeting a gene of interest using BLASTp with a relatively high bit score and identity cut-off so all of the sequences to be aligned are very similar. I need to create an alignment to check for mutations based on their position in a reference ...
written 4.6 years ago by weslfield90
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Pairwise vs. Multiple Sequence Alignments: Which has better accuracy?
... I am aligning many similar sequences from a BLAST result and looking for mutations at certain positions. My inclination is that an MSA (Clustal Omega) is the best approach but my PI is worried about misalignments and believes that Pairwise alignments against a reference sequence would be the best ap ...
pairwise alignment sequence msa blast written 4.6 years ago by weslfield90 • updated 3.5 years ago by Biostar ♦♦ 20
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Comment: C: Construct Newick Tree from tab-delimited or csv file of phylogeny, preferably in
... Thanks Asaf, the code below in my answer addressed the problem using the node approach.  תודה רבה מטכניון :) ...
written 4.6 years ago by weslfield90
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Answer: A: Construct Newick Tree from tab-delimited or csv file of phylogeny, preferably in
... import csv from collections import defaultdict from pprint import pprint def tree(): return defaultdict(tree) def tree_add(t, path): for node in path: t = t[node] def pprint_tree(tree_instance): def dicts(t): return {k: dicts(t[k]) for k in t} pprint(dicts(tree_instance)) def csv_ ...
written 4.6 years ago by weslfield90
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Construct Newick Tree from tab-delimited or csv file of phylogeny, preferably in Python
... So I am looking for a way, preferably a Pythonic way (packages are ok), to convert a tab-delimited or csv of hierarchical phylogenies into the classic Newick format for tree visualization. Each line of the file has ['Phylum','Class','Order','Family','Genus','Species','Subspecies','gi'] as values an ...
phylogeny python tree newick written 4.6 years ago by weslfield90 • updated 9 months ago by Biostar ♦♦ 20
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Translating Nucleotide MSA to Amino Acid MSA
... Hi, so I have a nucleotide mutliple sequence alignment that I would like to translate into an amino acid MSA based on the reading frame of a reference sequence in that alignment. Looking for the best way to do this, preferably a Biopython way. Thanks! ...
alignment sequence msa written 4.9 years ago by weslfield90 • updated 4.6 years ago by Whetting1.5k
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How Does The Metagenome Assembly Process Affect Snps?
... So I am doing some research focusing on certain SNPs of importance found within metagenomes. For example, within the human gut from data provided by the Human Microbiome Project (HMP). My questing is how does the process of contig assembly affect SNPs? Will some SNPs be masked by the assembly proces ...
ncbi assembly metagenomics snp written 5.1 years ago by weslfield90 • updated 5.1 years ago by umer.zeeshan.ijaz1.7k
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Comment: C: Rapid Querying Of Metagenomic Data Given A Reference Genome
... The metagenome data mostly, which is very large and very computationally intensive to search. JGI's IMG can do something similar to this in a very short amount of time probably by leveraging look-up tables and annotated genomes/metagenomes. https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=GenomeHi ...
written 5.1 years ago by weslfield90

Latest awards to weslfield

Popular Question 4.0 years ago, created a question with more than 1,000 views. For Biopython: Executing Blast On Custom Db
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Parsing Blast Results In Java
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Parsing Blast Results In Java
Student 4.6 years ago, asked a question with at least 3 up-votes. For Rapid Querying Of Metagenomic Data Given A Reference Genome

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