User: vkkodali

gravatar for vkkodali
vkkodali1.7k
Reputation:
1,680
Status:
Trusted
Location:
United States
Last seen:
3 hours ago
Joined:
3 years, 6 months ago
Email:
v*****@gmail.com

Posts by vkkodali

<prev • 188 results • page 1 of 19 • next >
0
votes
1
answer
66
views
1
answers
Answer: A: Using Entrez to find the taxonomy for an accession number
... Depending on what kind of accessions you have (GenBank, RefSeq or Swiss-Prot), you should be able to tell which database the accession is coming from. Take a look at [this page](https://www.ncbi.nlm.nih.gov/Sequin/acc.html). For example, all RefSeq proteins will have accessions in the format `[NAXWY ...
written 8 days ago by vkkodali1.7k
1
vote
3
answers
92
views
3
answers
Answer: C: How to download from ncbi not a whole FASTA file, but only a certain interval?
... [EDirect](http://bit.ly/entrez-direct) works well for a relatively small number of sequences. If the total number of accessions (column 2 of your table) you are dealing with is small, you may want to consider first downloading the entire fasta for those accessions and then using something like `bedt ...
written 14 days ago by vkkodali1.7k
1
vote
3
answers
226
views
3
answers
Answer: A: Fetching Genbank Assembly IDs with protein
... Thanks, I understand this better now. For this purpose, here's what I would do: 1. Download the entire list of GCA accessions 2. For each GCA accession, download the `feature_table.txt` file from NCBI FTP. For example, the `feature_table.txt` file for the assembly `GCA_002691735.1` is [here](https ...
written 19 days ago by vkkodali1.7k
0
votes
2
answers
124
views
2
answers
Comment: C: How to get GTF file for Rousettus_aegyptiacus?
... It looks like the annotation file and the genomic FASTA files do not have matching genomic seq-ids. If you use the following two files, I expect the seq-ids to be matching: Genomic FASTA: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/466/805/GCF_001466805.2_Raegyp2.0/GCF_001466805.2_Raegyp2.0_gen ...
written 27 days ago by vkkodali1.7k
0
votes
3
answers
226
views
3
answers
Comment: C: Fetching Genbank Assembly IDs with protein
... What is it that you are looking for in the end? You can search the ‘assembly’ database and fetch summary about the assembly but that won't get you the sequence. If you want A specific sequence then you need to figure out which sequence it is you want from the assembly because an assembly can have mo ...
written 27 days ago by vkkodali1.7k
2
votes
3
answers
226
views
3
answers
Answer: A: Fetching Genbank Assembly IDs with protein
... Since you already have accessions, try the following: from Bio import Entrez,SeqIO Entrez.email = 'xxx@yyy.zzz' handle = Entrez.efetch(id = 'MAG94467.1', db = 'protein', rettype='gb', retmode='text') record = SeqIO.read(handle, 'genbank') print(record) ...
written 27 days ago by vkkodali1.7k
2
votes
2
answers
118
views
2
answers
Answer: A: How to parse sequences from a gbk file, based on the coordinates specified in gi
... If you need the sequence for that list of coordinates in FASTA format and based on your screenshot it appears to be a sequence available at NCBI, you can use [Entrez Direct](https://bit.ly/entrez-direct) as follows: $ cat temp.txt 638483-646063 1137523-1143403 1182782-1250536 ...
written 28 days ago by vkkodali1.7k
0
votes
2
answers
124
views
2
answers
Answer: A: How to get GTF file for Rousettus_aegyptiacus?
... You can download the GTF file from NCBI by searching for `Rousettus aegyptiacus` in the [NCBI Assembly portal](https://www.ncbi.nlm.nih.gov/assembly), select the top hit use the blue Download button as shown in the image below: ![enter image description here][1] [1]: https://i.postimg.cc/mr85CQ ...
written 28 days ago by vkkodali1.7k
1
vote
4
answers
142
views
4
answers
Answer: A: How to download fasta files of a particular genus bacteria available in NCBI?
... Go to https://www.ncbi.nlm.nih.gov/genome/539 and click on the 'Assembly' link on the right hand side. It will take you to the [Assembly page](https://www.ncbi.nlm.nih.gov/assembly?LinkName=genome_assembly&from_uid=539) with the 8 linked assemblies. On this page, click on the blue 'Download Asse ...
written 5 weeks ago by vkkodali1.7k
0
votes
1
answer
135
views
1
answers
Comment: C: Is there any way to download knownCanonical set from the NCBI Refseq track as it
... In that case, RefSeq Select is your best option. Note, RefSeq Select is only available for protein-coding loci; so of the ~54k unique GeneIDs annotated currently, 19k are protein-coding and have a RefSeq Select. Are you interested in getting these data in GFF3 format? If so, you can either filter th ...
written 5 weeks ago by vkkodali1.7k

Latest awards to vkkodali

Appreciated 5 days ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Scholar 27 days 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 28 days 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 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?
Scholar 9 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?
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Teacher 10 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 10 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?
Scholar 12 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?
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Obtain N50 stats from NCBI for all Hymenoptera genome assemblies
Teacher 12 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?
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?
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?
Scholar 4 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 5 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?
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 10 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 11 months ago, received more than 100 upvotes.
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Change NBCI accession numbers to UNIPROT identifiers

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2071 users visited in the last hour