User: sharmatina189059
sharmatina189059 • 30
- Reputation:
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- United States
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- 6 days, 13 hours ago
- Joined:
- 3 years, 1 month ago
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Posts by sharmatina189059
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... Dear all
I have a genome sequence for which i have a different coordinate file like this:
AXXXX_XXXX 251962 252762 TnAs3 250165 250795 TnAs3 250791 250838
I need to make a figure representing the genome annotation of these 3 coordinates within min. coordinate range to max. coordinate range. How ca ...
written 11 days ago by
sharmatina189059 • 30
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... Hi
Sibelia is used for comparing only two genomes. I can not use it for multiple genomes. ...
written 12 days ago by
sharmatina189059 • 30
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5 follow
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... Dear all
I have some protein sequences and bacterial genomes. I need to have a figure showing a block diagram of upstream and dowstream genes of that particular gene within multiple bacterial genome. Is there any tool for making a synteny of one gene in multiple genomes of bacteria? ...
written 12 days ago by
sharmatina189059 • 30
• updated
12 days ago by
Joseph Hughes • 2.6k
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Comment:
C: how to change fasta headers?
... But I have retrieved it from NCBI ftp site and the format is same.
AM I doing some error? ...
written 11 weeks ago by
sharmatina189059 • 30
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Comment:
C: how to change fasta headers?
... I have edited my post. Thanks!! ...
written 11 weeks ago by
sharmatina189059 • 30
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Comment:
C: how to change fasta headers?
... and if the sequences are like
>WP_000580188.1hypotheticalprotein[Acinetobacterbaumannii]
MIGQQRNILATLGIDVWIPRTQVCQKNNAHTLWRDQVVEPHESITVPTIDVPAFEQKNTQPQVLEIPKVVEEPPIVVAEVSQPEILVEKPKVIEQETITPFELQAYCLEKCVIFVDVTALETEEKQLWANIQKAKVGQYSELRWPFPLAAYQDQRGVGSYIQGFLDAVAAEKKILCLGKCTYIQHANIIHLASLKEML ...
written 11 weeks ago by
sharmatina189059 • 30
• updated
11 weeks ago by
finswimmer ♦ 7.7k
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201
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3
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Comment:
C: how to change fasta headers?
... Thanku so much it really works!! ...
written 11 weeks ago by
sharmatina189059 • 30
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... Dear all
I have a file containing multiple fasta sequnces like
>lcl|NZ_CP018664.1_prot_WP_000637306.1_3741 [locus_tag=AUO97_RS19225] [protein=hypothetical protein] [protein_id=WP_000637306.1] [location=complement(4001198..4001389)] [gbkey=CDS]
MIVSNNFAVPYYLNVRKEKGMTAYYWATHQSQLALFDSYELAY ...
written 11 weeks ago by
sharmatina189059 • 30
• updated
11 weeks ago by
Hugo • 140
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... I am running this command
`ncbi-genome-download -l complete,chromosome bacteria --genus "Acinetobacter baumannii" --format protein-fasta`
but this gives me MD5SUMS file names like this. I need fasta sequnces.
260ac38772d1f9d98641f03bc5b07596 ./GCF_000018445.1_ASM1844v1_assembly_report.txt
...
written 12 weeks ago by
sharmatina189059 • 30
• updated
12 weeks ago by
jrj.healey ♦ 9.1k
2
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222
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1
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... How can I download all protein sequences of complete genome sequences of Acinetobacter baumannii from ncbi ftp site? ...
written 12 weeks ago by
sharmatina189059 • 30
• updated
12 weeks ago by
jrj.healey ♦ 9.1k
Latest awards to sharmatina189059
Popular Question
12 days ago,
created a question with more than 1,000 views.
For genbank file parsing
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For genbank file parsing
Popular Question
11 weeks ago,
created a question with more than 1,000 views.
For blast alignemnt query coverage
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