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0
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2
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710
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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 43k • written 10 months ago by ▴ 120
8
votes
9
replies
1.4k
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 16 months ago by 43k • written 23 months ago by ▴ 120
0
votes
0
replies
385
views
How to calculate Heaps Alpha value from the roary pangenome analysis ?
NGS pan-genome genome proteins
updated 16 months ago by 43k • written 2.1 years ago by ▴ 120
0
votes
0
replies
532
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 2.8 years ago by ▴ 40 • written 4.9 years ago by ▴ 120
2
votes
1
reply
591
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics cytoscape network STRING
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 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 • 0 • written 3.1 years ago by ▴ 120
1
vote
2
replies
756
views
Any pipeline/tool to predict fungal virulence factors ?
gene genome sequence
updated 10 months ago by 43k • written 2.9 years ago by ▴ 120
0
votes
0
replies
580
views
Tool/server for metal ion amino acid binding site prediction ?
proteomics database python genomics
updated 2.8 years ago by 43k • written 2.9 years ago by ▴ 120
2
votes
1
reply
1.3k
views
how to define open-pangenome?
python fasta genome dna clustering
updated 3.0 years ago by ▴ 20 • written 3.1 years ago by ▴ 120
0
votes
0
replies
621
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
823
views
How to parse all the Zn-binding protein sequences from MetalPDB?
PDB database NCBI protein python
3.0 years ago by Kumar ▴ 120
5
votes
1
reply
779
views
How to evaluate phylogenetic congruence between two phylogenetic tree?
snp python perl genomics phylogeny
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 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 8.5k • written 3.1 years ago by ▴ 120
15
votes
10
replies
7.2k
views
9 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 3.1 years ago by 8.5k • written 3.1 years ago by ▴ 120
3
votes
5
replies
2.1k
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 ★ 27k • written 3.2 years ago by ▴ 120
0
votes
0
replies
874
views
How to incorporate outgroup organism for whole genome SNP based phylogeny?
alignment genome SNP phylogeny phylogenetics
3.2 years ago by Kumar ▴ 120
0
votes
0
replies
697
views
error in Islandviewer4 API.
software-error perl python sequence
updated 13 months ago by 43k • written 3.3 years ago by ▴ 120
2
votes
3
replies
1.4k
views
What is the difference between Average Nucleotide Identity (ANI) and blastn analysis?
alignment blast sequence
updated 13 months ago by 43k • written 3.3 years ago by ▴ 120
8
votes
14
replies
2.4k
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 7 months ago by 21k • written 3.5 years ago by ▴ 120
0
votes
2
replies
1.2k
views
error while executing panX script (KeyError: 'db_xref').
linux python genome biopython
updated 10 months ago by 43k • written 3.7 years ago by ▴ 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 10 months ago by 43k • written 3.6 years ago by ▴ 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
1.0k
views
How to upload accessory_binary_genes.fa.newick and gene_presence_absence.csv files in Phandango?
software-error python SNP roary
updated 10 months ago by 43k • written 3.6 years ago by ▴ 120
1
vote
2
replies
1.3k
views
What is the minimum percentage of identity (blastp) to predict the orthologous genes in different species?
Assembly gene genome alignment
updated 10 months ago by 43k • written 3.6 years ago by ▴ 120
0
votes
2
replies
3.0k
views
How to convert gbk file to roary tool acceptable gff3 format?
linux bash python perl
updated 10 months ago by 43k • written 3.6 years ago by ▴ 120
2
votes
3
replies
3.1k
views
Error in npm installation and start.
python linux bash R software error
updated 3.7 years ago by 35k • written 3.7 years ago by ▴ 120
0
votes
2
replies
774
views
Error in pan-genome-analysis tool panX.
bash python genome perl
updated 10 months ago by 43k • written 3.7 years ago by ▴ 120
6
votes
8
replies
1.4k
views
How to remove poor quality sequences from a fasta file?
perl python shell bash fasta
3.7 years ago by Kumar ▴ 120
1
vote
2
replies
3.4k
views
Is there any tool available to generate ultrametric tree from a rooted phylogenetic tree?
phylogeny perl python R unix
updated 4.2 years ago by ★ 3.8k • written 4.2 years ago by ▴ 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 4.2 years ago by 15k • written 4.2 years ago by ▴ 120
7
votes
13
replies
3.1k
views
How to concatenate clustalw aligned fasta sequence?
alignment fasta sequence clustalw
updated 4.2 years ago by 8.4k • written 4.2 years ago by ▴ 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 ★ 3.7k • written 4.3 years ago by ▴ 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 141k • written 4.3 years ago by ▴ 120
3
votes
2
replies
1.6k
views
What is the meaning of final ML optimization likelihood value in raxml phylogenetic analysis?
phylogeny raxml evolution diversity analysis
updated 4.3 years ago by ★ 27k • written 4.3 years ago by ▴ 120
0
votes
4
replies
793
views
Error in PGAP pangenome pipeline?
sequence genome sequencing gene
updated 10 months ago by 43k • written 4.4 years ago by ▴ 120
2
votes
6
replies
887
views
How to identify the corresponding gene of a short sequence of a genome?
fasta gene genome sequence
updated 10 months ago by 43k • written 4.4 years ago by ▴ 120
2
votes
1
reply
1.2k
views
Blastn is not working for short sequences?
software-error fasta blast sequence
updated 10 months ago by 43k • written 4.4 years ago by ▴ 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 ★ 2.0k • written 4.5 years ago by ▴ 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 10 months ago by 43k • written 4.5 years ago by ▴ 120
1
vote
2
replies
630
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly gene genome next-gen
updated 10 months ago by 43k • written 4.5 years ago by ▴ 120
2
votes
4
replies
818
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 10 months ago by 43k • written 4.6 years ago by ▴ 120
2
votes
3
replies
1.2k
views
issue with fastQ reads download from NCBI-SRA database?
SRA fastq ngs sequencing NCBI
updated 4.6 years ago by ▴ 130 • written 4.6 years ago by ▴ 120
0
votes
1
reply
1.4k
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
916
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 43k • written 4.8 years ago by ▴ 120
0
votes
1
reply
1.4k
views
Best tool for bacterial genomic island prediction?
genome genomic-island
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
13
votes
3
replies
29k
views
What is the difference between blastx and tblastn?
assembly blast ncbi sequence
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
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