User: vkkodali

gravatar for vkkodali
vkkodali1.1k
Reputation:
1,140
Status:
Trusted
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
3 years ago
Email:
v*****@gmail.com

Posts by vkkodali

<prev • 125 results • page 1 of 13 • next >
0
votes
1
answer
143
views
1
answers
Comment: C: How to define blast online to filter out PREDICTED and hypothetical proteins
... Perhaps you can add use the option to exclude the XM/XP models? If this is a computationally expensive search, you may just want to stick to the solution of jrj.healey and filter the results after the fact. That way, if you ever need the entire result set, you can always go back to it without having ...
written 6 weeks ago by vkkodali1.1k
0
votes
1
answer
161
views
1
answers
Answer: A: Extracting blocks features by their coordinates in a genome (using BioPython)?
... You can use the [Entrez Direct][1] tool `efetch` as follows: efetch -db nuccore -id BA000007.3 -format gb -seq_start 1443423 -seq_stop 1444553 This will return a genbank flat file with the two partial gene features. This translates to the following in biopython: with Entrez.efetch(db="n ...
written 7 weeks ago by vkkodali1.1k
3
votes
3
answers
167
views
3
answers
Answer: A: Download All The Bacterial Genomes of Pseudomonas aeruginosa From Ncbi
... Since all the other answers appear to be command-line based, here's a point-and-click method. Follow the link to the NCBI Genomes page you have provided in your post (https://www.ncbi.nlm.nih.gov/genome/?term=pseudomonas%20aeruginosa) and click on the 'Assembly' link in the 'Related Information' pan ...
written 11 weeks ago by vkkodali1.1k
0
votes
1
answer
1.1k
views
1
answers
Answer: A: Multiple protein accession number query Command LIne Blastp
... You can use [Entrez Direct](http://bit.ly/entrez-direct) to download the sequences in fasta format on the fly like this: blastp -query <(epost -db protein -input | efetch -format fasta) -db The `acc_list.txt` file should contain valid protein accessions, one per line. ...
written 12 weeks ago by vkkodali1.1k
2
votes
2
answers
238
views
2
answers
Comment: C: What is the difference between SRR, DRR, ERR ?
... > P – Publication Actually, P is for Project here. There can be an SRP study that has not been published at all. ...
written 12 weeks ago by vkkodali1.1k
0
votes
2
answers
170
views
2
answers
Answer: A: Downloading set of fasta sequences based on gene id
... Use [Entrez Direct](http://bit.ly/entrez-direct). See: https://www.biostars.org/p/345772 ...
written 12 weeks ago by vkkodali1.1k
2
votes
2
answers
238
views
2
answers
Answer: A: retrieving only one result using entrez direct
... Add `-stop 5` to your `efetch` to limit to 5 hits. ...
written 3 months ago by vkkodali1.1k
1
vote
2
answers
376
views
2
answers
Comment: C: Convert RefseqID to EntrezID
... Since you are interested in Entrez IDs and starting with RefSeq accessions, why not use an NCBI tool? EDirect works fine for this. printf 'XR_002293119.2\nXM_004081009.3\nXM_023961859.1' \ | epost -db nuccore -format acc \ | elink -db nuccore -target gene -name nuccore_gene \ ...
written 3 months ago by vkkodali1.1k
0
votes
2
answers
376
views
2
answers
Answer: A: Convert RefseqID to EntrezID
... ## Point-and-click 1. Go to [Batch Entrez](https://www.ncbi.nlm.nih.gov/sites/batchentrez) and upload your list of RefSeq accessions. Choose 'Nucleotide' as the database. Click the 'Retrieve' button. 2. Once you are in the results page, you will find 'Find related data' widget on the right hand side ...
written 3 months ago by vkkodali1.1k
1
vote
1
answer
266
views
1
answers
Answer: A: Annotate CpG Islands for a new genome
... See: https://www.biostars.org/p/349994/#350026 ...
written 4 months ago by vkkodali1.1k

Latest awards to vkkodali

Scholar 11 weeks ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 3 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Guru 5 months ago, received more than 100 upvotes.
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Change NBCI accession numbers to UNIPROT identifiers
Centurion 6 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 7 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 7 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 7 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 8 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 9 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 9 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 9 months ago, created an answer that has been accepted. For C: How do I set filter for NCBI esearch to get fasta for Genes only?
Scholar 9 months ago, created an answer that has been accepted. For C: Strange esearch behavior

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 561 users visited in the last hour