User: massa.kassa.sc3na

Reputation:
250
Status:
Trusted
Location:
Last seen:
5 days, 9 hours ago
Joined:
3 years, 6 months ago
Email:
m****************@gmail.com

Posts by massa.kassa.sc3na

<prev • 57 results • page 1 of 6 • next >
0
votes
0
answers
85
views
0
answers
Comment: C: Using MEMEChip for finding transcription factor binding sites motifs
... The task before you greatly depends on data quality you have and how well conserved the motifs you are after are. It is my understanding that for meme-chip, you provide the whole peaks, not only some cut-out region. If you are confident about the motif position, then do the cut-out and use meme di ...
written 4 weeks ago by massa.kassa.sc3na250
2
votes
1
answer
110
views
1
answers
Comment: C: NT database update (number of files)
... You may notice, that current `nt.xx.tar.gz` has almost 3GB which is about 3 times the size of the old nt part. ...
written 4 weeks ago by massa.kassa.sc3na250
0
votes
1
answer
176
views
1
answers
Comment: C: How to obtain all accession.version identifiers for a BLAST database using ENTRE
... Yes I agree, I've also tested it on db v5. ...
written 7 weeks ago by massa.kassa.sc3na250
0
votes
1
answer
176
views
1
answers
Answer: A: How to obtain all accession.version identifiers for a BLAST database using ENTRE
... To anybody who might want to retrieve accessions from BLAST database without downloading whole database. I didn't find any route through ENTREZ, however, I've found that you don't need the whole BLAST database to retrieve the accessions for the sequences. Only the `.nhr`, `.nin` and `.nal` (`.ndb ...
written 7 weeks ago by massa.kassa.sc3na250
0
votes
0
answers
108
views
0
answers
Comment: C: Biopython HTTPError when Fetching more than 1400 Entries from NCBI
... From my experience, you don't need epost. Just join eg 100 ids, and pass them to efetch. I wouldn't put much more id's at one time. For example I'm using this construction to fetch fasta sequences without problem: with Entrez.efetch(db='nucleotide', id=','.join(aclist), rettype='fasta', retmod ...
written 9 weeks ago by massa.kassa.sc3na250
0
votes
0
answers
232
views
0
answers
Comment: C: How can I count aminoacid residues from a HUGE compressed fasta file?
... I think that the modified code does just that - iteratively (sequence-wise) update the dict (`Counter`) object. Without the need to hold the decompressed data on the disc. But I could be wrong. ...
written 3 months ago by massa.kassa.sc3na250
1
vote
0
answers
232
views
0
answers
Comment: C: How can I count aminoacid residues from a HUGE compressed fasta file?
... You are almost there: ``` def element_count(filename): """Returns a dicitonary Counter with the counting if the aac that compose the sequences from a gzip fasta file. The aacs as keys and counts as values.""" with gzip.open(filename, "rt") as handle: aac_count = Counter() ...
written 3 months ago by massa.kassa.sc3na250
0
votes
1
answer
173
views
1
answers
Comment: C: Why is asn2fasta so slow compared to efetch (when the sequence is not part of as
... Yes, the annotwriter gives me acceptable performance - I didn't even notice that there are remote lookups with annotwriter. I'll contact the NCBI's help desk and see if they have any insight. Thank you ...
written 3 months ago by massa.kassa.sc3na250
1
vote
1
answer
204
views
1
answers
Comment: C: Programatically (Python) Navigate from BLASTp results to Genbank file
... First things first - ncbi has many different databases, here I've used `nuccore` and `protein`, each holding respective records (nucleotide and protein). The `nuccore` db does not contain any proteins ( protein accession numbers ) so you need to give it nucleotide accession number - in your case, th ...
written 3 months ago by massa.kassa.sc3na250
0
votes
1
answer
173
views
1
answers
Comment: C: Why is asn2fasta so slow compared to efetch (when the sequence is not part of as
... Thank you for the answer. I'm aware that I can download prepossessed gff files from ncbi (and it is the path I'm using for the bulk of the data). The stated path is intended as complementary route for accessions which were not part of the initial data fetch (and are not present locally). The prob ...
written 3 months ago by massa.kassa.sc3na250

Latest awards to massa.kassa.sc3na

Scholar 3 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 3 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Programatically (Python) Navigate from BLASTp results to Genbank file
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: rRNA and bacteria: Absence and duplicates
Scholar 4 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 5 months ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 9 months ago, created an answer that has been accepted. For C: BLAST using Biopython

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1656 users visited in the last hour