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questions
0
votes
2
replies
725
views
What are the offline tools available for the Eukaryotic genome annotation (including fungi, algae, animal and plant ) ?
Assembly
genes
genome
Annotation
updated 10 months ago by
Ram
43k • written 10 months ago by
Kumar
▴ 120
8
votes
9
replies
1.5k
views
How to obtain gtf file for plant genomes?
Ensembl
Assembly
RNA-seq
Gene
Genome
10 months ago by
Kumar
▴ 120
1
vote
2
replies
1.7k
views
How to interpret two letter codes of COG category obtained from EggNOG tool?
Assembly
genome
proteins
genes
updated 17 months ago by
Ram
43k • written 23 months ago by
Kumar
▴ 120
0
votes
0
replies
389
views
How to calculate Heaps Alpha value from the roary pangenome analysis ?
NGS
pan-genome
genome
proteins
updated 17 months ago by
Ram
43k • written 2.2 years ago by
Kumar
▴ 120
0
votes
0
replies
538
views
Is there any way to customise the colour codes for multiple-sequence alignment (MSA)?
alignment
Python
genomics
R
phylogeny
2.7 years ago by
Kumar
▴ 120
5
votes
6
replies
2.1k
views
issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
r
bioconductor
alignment
R
sequencing
updated 2.9 years ago by
Biodeer
▴ 40 • written 4.9 years ago by
Kumar
▴ 120
2
votes
1
reply
602
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics
cytoscape
network
STRING
updated 2.9 years ago by
Ram
43k • written 2.9 years ago by
Kumar
▴ 120
0
votes
1
reply
1.2k
views
error in anvi'o tool
python
software error
genome
R
gene
updated 2.9 years ago by
Iva
• 0 • written 3.2 years ago by
Kumar
▴ 120
1
vote
2
replies
762
views
Any pipeline/tool to predict fungal virulence factors ?
gene
genome
sequence
updated 11 months ago by
Ram
43k • written 3.0 years ago by
Kumar
▴ 120
0
votes
0
replies
586
views
Tool/server for metal ion amino acid binding site prediction ?
proteomics
database
python
genomics
updated 2.9 years ago by
Ram
43k • written 3.0 years ago by
Kumar
▴ 120
2
votes
1
reply
1.3k
views
how to define open-pangenome?
python
fasta
genome
dna
clustering
updated 3.0 years ago by
Nelly
▴ 20 • written 3.1 years ago by
Kumar
▴ 120
0
votes
0
replies
626
views
Assembly pipeline/tutorial for SMRT (PacBio) sequenced bacterial genome data?
python
perl
pipeline
genome
sequence
2.9 years ago by
Kumar
▴ 120
1
vote
2
replies
832
views
How to parse all the Zn-binding protein sequences from MetalPDB?
PDB
database
NCBI
protein
python
3.1 years ago by
Kumar
▴ 120
5
votes
1
reply
787
views
How to evaluate phylogenetic congruence between two phylogenetic tree?
snp
python
perl
genomics
phylogeny
updated 3.1 years ago by
Mensur Dlakic
★ 27k • written 3.1 years ago by
Kumar
▴ 120
2
votes
2
replies
1.2k
views
How to predict GC-Content percentage of a fasta file?
fasta
python3
perl
python
genome
updated 3.1 years ago by
Juke34
8.6k • written 3.1 years ago by
Kumar
▴ 120
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 13 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
3
votes
5
replies
2.2k
views
How to parse protein and dna sequences from prokka generated gbk or gff file based on locus_tag?
genome
perl
python
bash
R
updated 3.2 years ago by
Mensur Dlakic
★ 27k • written 3.2 years ago by
Kumar
▴ 120
0
votes
0
replies
880
views
How to incorporate outgroup organism for whole genome SNP based phylogeny?
alignment
genome
SNP
phylogeny
phylogenetics
3.3 years ago by
Kumar
▴ 120
0
votes
0
replies
702
views
error in Islandviewer4 API.
software-error
perl
python
sequence
updated 14 months ago by
Ram
43k • written 3.3 years ago by
Kumar
▴ 120
2
votes
3
replies
1.5k
views
What is the difference between Average Nucleotide Identity (ANI) and blastn analysis?
alignment
blast
sequence
updated 14 months ago by
Ram
43k • written 3.3 years ago by
Kumar
▴ 120
8
votes
14
replies
2.5k
views
How to remove fasta headers in a multifasta file and write file name as a fasta header?
gene
sequence
genome
alignment
next-gen
updated 8 months ago by
Joe
21k • written 3.6 years ago by
Kumar
▴ 120
0
votes
2
replies
1.2k
views
error while executing panX script (KeyError: 'db_xref').
linux
python
genome
biopython
updated 11 months ago by
Ram
43k • written 3.7 years ago by
Kumar
▴ 120
2
votes
4
replies
1.1k
views
Anybody knows any stand alone tool/pipeline for Bacterial Gene Ontology (GO) analysis?
gene
genome
sequence
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Kumar
▴ 120
7
votes
17
replies
2.0k
views
How to generate reverse complement for the fasta sequences specified in the given csv file?
python
perl
bash
shell
fasta
3.6 years ago by
Kumar
▴ 120
0
votes
0
replies
1.1k
views
How to upload accessory_binary_genes.fa.newick and gene_presence_absence.csv files in Phandango?
software-error
python
SNP
roary
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Kumar
▴ 120
1
vote
2
replies
1.4k
views
What is the minimum percentage of identity (blastp) to predict the orthologous genes in different species?
Assembly
gene
genome
alignment
updated 11 months ago by
Ram
43k • written 3.7 years ago by
Kumar
▴ 120
0
votes
2
replies
3.1k
views
How to convert gbk file to roary tool acceptable gff3 format?
linux
bash
python
perl
updated 11 months ago by
Ram
43k • written 3.7 years ago by
Kumar
▴ 120
2
votes
3
replies
3.1k
views
Error in npm installation and start.
python
linux
bash
R
software error
updated 3.8 years ago by
h.mon
35k • written 3.8 years ago by
Kumar
▴ 120
0
votes
2
replies
785
views
Error in pan-genome-analysis tool panX.
bash
python
genome
perl
updated 11 months ago by
Ram
43k • written 3.8 years ago by
Kumar
▴ 120
6
votes
8
replies
1.5k
views
How to remove poor quality sequences from a fasta file?
perl
python
shell
bash
fasta
3.8 years ago by
Kumar
▴ 120
1
vote
2
replies
3.5k
views
Is there any tool available to generate ultrametric tree from a rooted phylogenetic tree?
phylogeny
perl
python
R
unix
updated 4.3 years ago by
Brice Sarver
★ 3.8k • written 4.3 years ago by
Kumar
▴ 120
2
votes
2
replies
1.4k
views
How to specify codon based multiple sequence alignment in clustalw command line?
clustalw
fasta
alignment
sequence
gene
updated 4.3 years ago by
lieven.sterck
15k • written 4.3 years ago by
Kumar
▴ 120
7
votes
13
replies
3.2k
views
How to concatenate clustalw aligned fasta sequence?
alignment
fasta
sequence
clustalw
updated 4.3 years ago by
shenwei356
8.5k • written 4.3 years ago by
Kumar
▴ 120
4
votes
4
replies
1.9k
views
How to parse sequences from a gbk file, based on the coordinates specified in given file?
perl
python
bash
gbk
updated 4.3 years ago by
vkkodali_ncbi
★ 3.7k • written 4.3 years ago by
Kumar
▴ 120
3
votes
1
reply
1.3k
views
Is it possible to specify CPU/thread in raxmlHPC?
phylogenetics
raxml
gene
genetics
evolution
updated 4.3 years ago by
GenoMax
142k • written 4.3 years ago by
Kumar
▴ 120
3
votes
2
replies
1.7k
views
What is the meaning of final ML optimization likelihood value in raxml phylogenetic analysis?
phylogeny
raxml
evolution
diversity analysis
updated 4.4 years ago by
Mensur Dlakic
★ 27k • written 4.4 years ago by
Kumar
▴ 120
0
votes
4
replies
811
views
Error in PGAP pangenome pipeline?
sequence
genome
sequencing
gene
updated 11 months ago by
Ram
43k • written 4.4 years ago by
Kumar
▴ 120
2
votes
6
replies
905
views
How to identify the corresponding gene of a short sequence of a genome?
fasta
gene
genome
sequence
updated 11 months ago by
Ram
43k • written 4.5 years ago by
Kumar
▴ 120
2
votes
1
reply
1.2k
views
Blastn is not working for short sequences?
software-error
fasta
blast
sequence
updated 11 months ago by
Ram
43k • written 4.5 years ago by
Kumar
▴ 120
14
votes
14
replies
2.0k
views
Extract sequences consecutively from a large fasta files and save in new fasta files
python
perl
shell
r
fasta
updated 4.5 years ago by
Chirag Parsania
★ 2.0k • written 4.5 years ago by
Kumar
▴ 120
1
vote
3
replies
1.7k
views
Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?
Assembly
alignment
software-error
updated 11 months ago by
Ram
43k • written 4.5 years ago by
Kumar
▴ 120
1
vote
2
replies
642
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly
gene
genome
next-gen
updated 11 months ago by
Ram
43k • written 4.6 years ago by
Kumar
▴ 120
2
votes
4
replies
833
views
How to get the extended unaligned bases at the end of the read in reference based genome assembly?
Assembly
next-gen
alignment
genome
sequencing
4.6 years ago by
Kumar
▴ 120
4
votes
8
replies
2.0k
views
How to extract promoter sequences from a plant draft genome?
promoter
genome
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Kumar
▴ 120
2
votes
3
replies
1.3k
views
issue with fastQ reads download from NCBI-SRA database?
SRA
fastq
ngs
sequencing
NCBI
updated 4.7 years ago by
Researcher
▴ 130 • written 4.7 years ago by
Kumar
▴ 120
0
votes
1
reply
1.5k
views
samtools mpileup: bam file to consensus sequence generation error?
Assembly
genome
ngs
samtools
bcftools
4.7 years ago by
Kumar
▴ 120
4
votes
3
replies
930
views
What is the minimum number/threshold of gaps (NNNNNN) permitted in a draft genome?
Assembly
genome
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
0
votes
1
reply
1.4k
views
Best tool for bacterial genomic island prediction?
genome
genomic-island
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
13
votes
3
replies
29k
views
What is the difference between blastx and tblastn?
assembly
blast
ncbi
sequence
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny
genome
alignment
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
68 results • Page
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