User: mgalactus

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mgalactus730
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United Kingdom
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http://marcogalardini....
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mgalactus
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2 years, 10 months ago
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8 years ago
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Posts by mgalactus

<prev • 54 results • page 1 of 6 • next >
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Answer: A: Retriving compounds name from KEGG IDs
... You can either search for them [in the KEGG database website][1], or use something more automated like [the KEGG REST API][2] (in this specific case you need the "get" method). Suppose you are interested in the following three compound IDs: - C00818 - C00140 - C00259 Simply go to this webpage ...
written 4.1 years ago by mgalactus730
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Comment: C: A Quick Way To Annotate Entire Bacterial Genomes To Go?
... Hi, I actually think that the new beta feature of EggNOG could be way faster snd more useful: http://beta-eggnogdb.embl.de/#/app/seqmapper and code here: https://github.com/jhcepas/eggnog-mapper ...
written 4.2 years ago by mgalactus730
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Answer: A: Extracting more features from EMBL files with Biopython
... Hi, the 'product' annotation can be found inside each SeqFeature objects in the 'qualifiers' dictionary from Bio import SeqIO s = SeqIO.read('input.embl', 'embl') for feature in s.features: print(feature.qualifiers.get('product', [])) You can also filter the SeqFeature objects by type (fea ...
written 4.7 years ago by mgalactus730
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Comment: C: Biopython's GenomeDiagram input files???
... can you post the code you've used with your genbank file? ...
written 4.7 years ago by mgalactus730
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Answer: A: Biopython's GenomeDiagram input files???
... Hi, Sure, you can use fasta files to draw genome diagrams; you could provide the features you want to draw on top of the sequence from other files (say a gff file or a simple table you might have). You can convert a fasta file to a Genbank file with the following python script: from Bio import ...
written 4.7 years ago by mgalactus730 • updated 7 months ago by RamRS27k
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Comment: C: Kegg Data Download
... That requires a couple of steps: first retrieve the reaction IDs from KO IDs (example here) and then retrieve the entry for each reaction ID (example here); the EC number is under the field "ENZYME"   ...
written 4.9 years ago by mgalactus730
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Comment: C: Contiguator: A Bacterial Genomes Finishing Tool For Structural Insights On Draft
... Hi div, yes, CONTIGuator should be able to help you with that, granted that you have a closed reference genome (which should be the case for S. aureus). You also might want to try a new multiple genomes scaffolder called Medusa, which uses more than one reference genome to scaffold the contigs. ...
written 5.1 years ago by mgalactus730
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Comment: C: Print gene locations from a .gbk file
... My fault, it should have been "location" and not "locations" (I've updated the reply) ...
written 5.2 years ago by mgalactus730
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Answer: A: Print gene locations from a .gbk file
... Hi, the SeqFeature objects have a "location" attribute that contains the start/stop position of the feature. from Bio import SeqIO gbk_filename = "HS.gb" faa_filename = "HS_converted.faa" output_handle = open(faa_filename, "w") for seq_record in SeqIO.parse(gbk_filename, "genbank") : print ...
written 5.2 years ago by mgalactus730
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Comment: C: Bacterial GWAS analysis?
... Have a look at this recent review for some suggestions ...
written 5.2 years ago by mgalactus730

Latest awards to mgalactus

Great Question 3.3 years ago, created a question with more than 5,000 views. For Estimating Purifying Selection With Codeml (Paml)
Popular Question 3.4 years ago, created a question with more than 1,000 views. For A Quick Way To Annotate Entire Bacterial Genomes To Go?
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Kegg Data Download
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Print gene locations from a .gbk file
Student 4.2 years ago, asked a question with at least 3 up-votes. For It Is Wise To Transfer Kegg Annotations Between Orthologs?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Best Software For 454/Pacbio Hybrid Assembly
Popular Question 4.6 years ago, created a question with more than 1,000 views. For It Is Possible To Obtain A Sbml Model From Ec Numbers Or Kegg Reactions Identifiers?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Estimating Purifying Selection With Codeml (Paml)
Student 4.8 years ago, asked a question with at least 3 up-votes. For Estimating Purifying Selection With Codeml (Paml)
Popular Question 4.9 years ago, created a question with more than 1,000 views. For It Is Possible To Obtain A Sbml Model From Ec Numbers Or Kegg Reactions Identifiers?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For It Is Possible To Obtain A Sbml Model From Ec Numbers Or Kegg Reactions Identifiers?
Scholar 5.2 years ago, created an answer that has been accepted. For A: Print gene locations from a .gbk file
Teacher 5.2 years ago, created an answer with at least 3 up-votes. For A: Kegg Data Download
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Estimating Purifying Selection With Codeml (Paml)
Voter 5.6 years ago, voted more than 100 times.
Appreciated 6.3 years ago, created a post with more than 5 votes. For A: Kegg Data Download
Good Answer 6.3 years ago, created an answer that was upvoted at least 5 times. For A: Kegg Data Download
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Estimating Purifying Selection With Codeml (Paml)
Supporter 6.3 years ago, voted at least 25 times.
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: Kegg Data Download
Student 6.3 years ago, asked a question with at least 3 up-votes. For Is There A Tool For Bacterial Operon Prediction?
Student 6.3 years ago, asked a question with at least 3 up-votes. For What Is The Appropriate Order For A Background Model In Motif Searches?
Student 6.3 years ago, asked a question with at least 3 up-votes. For Estimating Purifying Selection With Codeml (Paml)

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