User: saadleeshehreen

Reputation:
70
Status:
Trusted
Location:
Last seen:
1 week, 1 day ago
Joined:
1 year, 11 months ago
Email:
s**************@gmail.com

Posts by saadleeshehreen

<prev • 86 results • page 1 of 9 • next >
0
votes
0
answers
112
views
0
answers
Comment: C: getting information from NCBI genebank files
... It could be any protein associated with anti-restriction. I am looking for a correlation between 'protein A' with anti-restriction proteins. I have already got 600 genomes having protein A. Now, trying to look at which of these genomes have anti-restriction proteins. ...
written 23 days ago by saadleeshehreen70
0
votes
0
answers
112
views
0
answers
getting information from NCBI genebank files
... Hi, I am interested to know about the presence of a specific protein called "anti restriction" in a list of ~600 genomes of different species of bacteria. It can be find from the NCBI genebank files. Manually checking those 600 genomes is time-consuming. Any suggestions on how can I know which of th ...
ncbi assembly genebank annotation written 23 days ago by saadleeshehreen70
5
votes
3
answers
149
views
3
answers
How to extract a particular region from a nucleotide contig?
... Hi, I have downloaded a contig from NCBI. It is around 100 kbp long and has a integrated prophage region. The prophage region is between 54501-90604 bp. How to extract only 54501-90604 bp from this contig? Cheers ...
assembly sequence written 3 months ago by saadleeshehreen70 • updated 3 months ago by Pierre Lindenbaum126k
1
vote
1
answer
209
views
1
answer
Retrieving organism name
... Hi, I usually use the following command to get GCF_id (Accession) from the NCBI. How Can I retrieve the "organism name/source" from NCBI? cat NZ_id.txt | while read i; do elink -db nuccore -id $i -target assembly|esummary| xtract -pattern DocumentSummary -element AssemblyAccession ; done ...
ncbi assembly e-utlilities written 7 months ago by saadleeshehreen70 • updated 7 months ago by SMK1.9k
0
votes
1
answer
234
views
1
answer
How to Deduplicate files
... Hi, I have list of 160111 protein files. Some of the files are duplication as GCA and GCF id contains same protein sequnces. How I can deduplicate the list on the basis of ASM102201v1? Enterobacter_hormaechei-158836#GCA_001022015.1/GCA_001022015.1_ASM102201v1_protein.faa Enterobacte ...
sequence written 10 months ago by saadleeshehreen70 • updated 10 months ago by finswimmer13k
0
votes
0
answers
228
views
0
answers
How to retrieve "Assembly statistics" for all (~4200) Pseudomonas aeruginosa genome from NCBI?
... Is any script/ source available to get genome size of all published Psedubomonas aeruginosa genomes from NCBI? This information is written in "Assembly statistics" Cheers ...
genome written 10 months ago by saadleeshehreen70 • updated 12 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
284
views
0
answers
How to solve the elink error ?
... Hi I am trying to get assembly number ( for example GCF_001166025.1 is for NZ_CQEB01000017.1) for 100 genomes with the following command. The command previously work for me but today giving some error. Anyone know what happen? elink -db nuccore -id NZ_CQEB01000017.1 -target assembly|esum ...
ncbi elink written 12 months ago by saadleeshehreen70
0
votes
2
answers
392
views
2
answers
How to fetch sequences from Proteinortho5 output containing all test species and no duplication in each genome
... Hi, I want to construct a phylogenic tree on 100 *Pseudomonas aeruginosa* genomes. Before constructing the tree, I want to first cluster those genomes on the basis of homology and for this purpose, I am using ProteinOrtho5 software. After running the software with synteny option I want to extract pr ...
proteinortho5 written 14 months ago by saadleeshehreen70 • updated 8 months ago by AlishaQ0
4
votes
2
answers
2.0k
views
5 follow
2
answers
Counting base and nucleotide frequency of multifasta file
... Hi, I have a mulifasta with 2000 sequences. The file is like this. >spacer_1 ATCCCGGGGGGTTTA............... >spacer_2 TCAGGTTT....... . . I want to count how many bases for each of them and what is the frequency of nucleotide (A,T,G,C) in each of the sequence. I tried ...
multifasta base count nucleotide frequency written 14 months ago by saadleeshehreen70 • updated 14 months ago by FX0
0
votes
0
answers
404
views
0
answers
Comment: C: Problem to run a perl script from shell
... same error message is showing ...
written 15 months ago by saadleeshehreen70

Latest awards to saadleeshehreen

Popular Question 3 months ago, created a question with more than 1,000 views. For grep things and counting line number in R
Popular Question 7 months ago, created a question with more than 1,000 views. For Building Hidden Markov Model (HMM) for proteins
Popular Question 7 months ago, created a question with more than 1,000 views. For gff to GFF3 converter
Popular Question 7 months ago, created a question with more than 1,000 views. For Counting base and nucleotide frequency of multifasta file
Popular Question 7 months ago, created a question with more than 1,000 views. For What is the meaning of alignment strand plus/minus in blastn?
Popular Question 10 months ago, created a question with more than 1,000 views. For grep things and counting line number in R
Popular Question 14 months ago, created a question with more than 1,000 views. For grep things and counting line number in R

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1583 users visited in the last hour