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6
votes
3
replies
5.5k
views
How to make ortholog table with Reciprocal Best Hit blast (Python?) ?
blast
genome
protein
gene
ortholog
updated 4.8 years ago by
Biostar
20 • written 8.1 years ago by
jolespin
▴ 150
0
votes
0
replies
4.5k
views
Comment:
C: tbl2asn Permission denied on Mac
updated 4.9 years ago by
Ram
44k • written 10.6 years ago by
jolespin
▴ 150
0
votes
0
replies
1.9k
views
Comment:
C: Find all genes in pathways associated with a target gene
updated 5.0 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
1
vote
2
replies
2.8k
views
Convert SBML to .sif for Cytoscape
cytoscape
network
sbml
updated 2.3 years ago by
Ram
44k • written 9.0 years ago by
jolespin
▴ 150
0
votes
1
reply
1.9k
views
Comment:
C: How to run Maple-2.3.0 (genome.jp) on the command-line?
7.5 years ago by
jolespin
▴ 150
0
votes
3
replies
1.9k
views
How to run Maple-2.3.0 (genome.jp) on the command-line?
kegg
modules
functional
fasta
maple
7.5 years ago by
jolespin
▴ 150
0
votes
1
reply
3.3k
views
How does WGCNA decide which genes are connected?
WGCNA
coexpression
gene
network
analysis
updated 7.7 years ago by
sina.nassiri
▴ 110 • written 8.6 years ago by
jolespin
▴ 150
1
vote
0
replies
1.7k
views
What are some robust correlation measures for network analysis?
network
robust
correlation
gene-expression
8.0 years ago by
jolespin
▴ 150
0
votes
7
replies
11k
views
Help creating .sqn file using tbl2asn to submit multiple sequences to Genbank
submit
batch
tbl2asn
sequence
genbank
updated 3.2 years ago by
Ram
44k • written 10.6 years ago by
jolespin
▴ 150
0
votes
0
replies
1.6k
views
Can someone describe how the SparCC corrected correlation measure works?
RNA-Seq
ChIP-Seq
genome
microbiome
metagenomics
8.1 years ago by
jolespin
▴ 150
2
votes
2
replies
6.0k
views
Download NCBI genome sequences from Python
genomics
genome
python
sequences
ncbi
updated 8.1 years ago by
Jenez
▴ 540 • written 8.1 years ago by
jolespin
▴ 150
0
votes
0
replies
1.5k
views
Find potential biological significance of a k-mer?
kmer
genome
sequence
dna
domain
8.1 years ago by
jolespin
▴ 150
2
votes
1
reply
3.3k
views
How to create a .SIF file?
interactome
gene
genome
RNA-Seq
protein
updated 2.6 years ago by
Ram
44k • written 9.0 years ago by
jolespin
▴ 150
4
votes
2
replies
3.8k
views
Use Python (e.g. mygene, biomart, db2db) to convert GO Terms to all genes in pathway
gene
python
ontology
mygene
pathway
updated 2.3 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
0
votes
0
replies
1.8k
views
How to interpret the SeqIO.parse record for GenBank features?
biopython
sequence
genome
genbank
parse
8.6 years ago by
jolespin
▴ 150
1
vote
1
reply
3.2k
views
Where to download complete Genbank file?
genbank
genome
gene
updated 20 months ago by
Ram
44k • written 8.6 years ago by
jolespin
▴ 150
0
votes
1
reply
2.1k
views
Gene ontology type analysis for pfam/tigrfams ?
hmm
gene
enrichment
ontology
pfam
8.7 years ago by
jolespin
▴ 150
0
votes
0
replies
1.4k
views
Convert from CyanoBase to Uniprot?
mapping
ontology
biomart
updated 16 months ago by
Ram
44k • written 8.8 years ago by
jolespin
▴ 150
1
vote
3
replies
1.9k
views
Find all genes in pathways associated with a target gene
gene
pathway
genome
kegg
systems-biology
updated 2.3 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
4
votes
6
replies
6.6k
views
DNA binding site motif database
gene
RNA-Seq
ChIP-Seq
genome
protein
updated 2.3 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
0
votes
1
reply
6.6k
views
Comment:
C: DNA binding site motif database
9.1 years ago by
jolespin
▴ 150
0
votes
1
reply
6.6k
views
Comment:
C: DNA binding site motif database
9.1 years ago by
jolespin
▴ 150
1
vote
1
reply
3.1k
views
How to normalize K-mer counts for genes of different length
gene
RNA-Seq
kmer
genome
sequence
updated 2.3 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
1
vote
1
reply
3.3k
views
Using BioPython to get sequences
gene
python
biopython
sequence
updated 2.3 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
2
votes
2
replies
1.9k
views
Determine which HUGO IDs are coding and non-coding
gene
blast
RNA-Seq
sequencing
genome
updated 2.3 years ago by
Ram
44k • written 9.1 years ago by
jolespin
▴ 150
0
votes
0
replies
4.3k
views
Comment:
C: Database to download HMMs for TIGRFAMS and PFAMS ?
9.2 years ago by
jolespin
▴ 150
0
votes
1
reply
4.3k
views
Comment:
Comment: Database to download HMMs for TIGRFAMS and PFAMS ?
updated 2.2 years ago by
Ram
44k • written 9.2 years ago by
jolespin
▴ 150
3
votes
4
replies
4.3k
views
Database to download HMMs for TIGRFAMS and PFAMS ?
hidden markov model
tigrfam
pfam
database
motif
updated 2.2 years ago by
Ram
44k • written 9.2 years ago by
jolespin
▴ 150
1
vote
2
replies
3.9k
views
contig with overlaps. how to circularize?
circular
dna
assembly
contig
genome
updated 2.2 years ago by
Ram
44k • written 9.3 years ago by
jolespin
▴ 150
2
votes
1
reply
2.0k
views
How to label non-CDS feature using genbank format for viewing in CLC
cds
genbank
clc
dna
updated 2.3 years ago by
Ram
44k • written 9.3 years ago by
jolespin
▴ 150
2
votes
0
replies
2.0k
views
Answer:
A: How to label non-CDS feature using genbank format for viewing in CLC
9.3 years ago by
jolespin
▴ 150
12
votes
8
replies
2.8k
views
6 follow
How else can one quantify a DNA sequence besides GC-content and length?
gc
seq
genome
gene
sequence
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
jolespin
▴ 150
0
votes
1
reply
2.8k
views
Comment:
Comment: How else can one quantify a DNA sequence besides GC-content and length?
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
jolespin
▴ 150
3
votes
2
replies
2.0k
views
Database that has all known proteins associated with a particular PFAM or TIGRFAM?
pfam
tigrfam
protein
database
gene
updated 2.1 years ago by
Ram
44k • written 9.3 years ago by
jolespin
▴ 150
0
votes
0
replies
1.6k
views
Does FragGeneScan find complete ORFs?
ORF
FragGeneScan
next-gen-sequencing
updated 24 months ago by
Ram
44k • written 9.4 years ago by
jolespin
▴ 150
5
votes
1
reply
1.8k
views
Database that says what genetic code a particular organism uses?
genome
gene
sequence
updated 2.0 years ago by
Ram
44k • written 9.4 years ago by
jolespin
▴ 150
0
votes
0
replies
2.3k
views
Full version of E. coli SBML model file ?
metabolism
sbml
updated 23 months ago by
Ram
44k • written 9.5 years ago by
jolespin
▴ 150
2
votes
3
replies
3.8k
views
Command line blast database problem
sequence
blast
alignment
software-error
updated 23 months ago by
Ram
44k • written 9.5 years ago by
jolespin
▴ 150
0
votes
1
reply
3.8k
views
Comment:
Comment: Command line blast database problem
updated 23 months ago by
Ram
44k • written 9.5 years ago by
jolespin
▴ 150
0
votes
0
replies
2.3k
views
Comment:
Comment: ATP = ADP + ATP_base? What is ATP_base?
updated 22 months ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
4
votes
2
replies
2.3k
views
ATP = ADP + ATP_base? What is ATP_base?
atp_base
metabolism
atp
updated 22 months ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
0
votes
0
replies
1.6k
views
Defining initial concentrations and rate equations in PySCeS ?
metabolic
kinetics
pysces
modeling
python
updated 3.1 years ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
1
vote
1
reply
1.9k
views
Losing all data after filter step using SGA
kmer
SGA
filter
assemly
updated 2.4 years ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
1
vote
0
replies
1.9k
views
Answer:
A: Losing all data after filter step using SGA
9.6 years ago by
jolespin
▴ 150
0
votes
0
replies
2.5k
views
Comment:
Comment: Tool to convert METATOOLS model file to SBML or .psc format
updated 2.4 years ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
1
vote
2
replies
2.5k
views
Tool to convert METATOOLS model file to SBML or .psc format
psc
sbml
metabolism
metatools
updated 2.4 years ago by
Ram
44k • written 9.7 years ago by
jolespin
▴ 150
1
vote
1
reply
2.7k
views
List all KEGG reaction IDs for organism with Orange.bio.kegg module Python
orange
python
kegg
reactions
updated 2.4 years ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
1
vote
0
replies
2.7k
views
Answer:
Answer: List all KEGG reaction IDs for organism with Orange.bio.kegg module Python
updated 2.4 years ago by
Ram
44k • written 9.6 years ago by
jolespin
▴ 150
2
votes
1
reply
2.4k
views
Python package similar to METATOOL 5.0 ?
metabolic
python
metabolism
modeling
updated 2.5 years ago by
Ram
44k • written 9.7 years ago by
jolespin
▴ 150
1
vote
0
replies
2.4k
views
Answer:
Answer: Python package similar to METATOOL 5.0 ?
updated 2.5 years ago by
Ram
44k • written 9.7 years ago by
jolespin
▴ 150
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