User: massa.kassa.sc3na

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Posts by massa.kassa.sc3na

<prev • 42 results • page 1 of 5 • next >
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Comment: C: rRNA and bacteria: Absence and duplicates
... Do you have the `Infernal` optional dependency installed (https://github.com/tseemann/prokka#optional)? The infernal together with Rfam database should be able to find the RNAs. ...
written 18 hours ago by massa.kassa.sc3na150
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Comment: C: How to obtain all accession.version identifiers for a BLAST database using ENTRE
... Thank you for the link. According to that it looks like there is no direct link between `blastdbinfo` and e.g. `nuccore`. ...
written 3 days ago by massa.kassa.sc3na150
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How to obtain all accession.version identifiers for a BLAST database using ENTREZ
... Hi all, background: I need to be able to recognize all possible sequence identifiers present in preformatted NCBI nucleotide databases. I've implemented regular expression following https://www.ncbi.nlm.nih.gov/Sequin/acc.html, but it is not enough. Other accessions (e.g. PDB) are also present. So ...
elink entrez blast written 3 days ago by massa.kassa.sc3na150
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Comment: C: gff3 header delimiter space or a tab
... Link to "official" (best I've found so far) specifications: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md ...
written 8 days ago by massa.kassa.sc3na150
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Comment: C: Entries Per File FASTA Splitter, not quite working
... What you are experiencing is because you increment the `Counter` after you've seen the header. Then you check if counter is specified value and write the file - while you have NOT yet read the sequence. You'll need to either set up some kind of buffer for reading one sequence completely (and then ...
written 11 days ago by massa.kassa.sc3na150
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Comment: C: Chunk That Fasta?
... You have to erase the `ToWrite` buffer after writing new file (you forgot to change it from `to_write = []` to `ToWrite = []`) ...
written 19 days ago by massa.kassa.sc3na150
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Answer: A: NCBI gene Dabase info extration
... Hi, it appears that the ontology annotation is for `Arabidopsis` provided by TAIR. You can download their database of GO terms. Look at https://www.arabidopsis.org/download_files/GO_and_PO_Annotations/Gene_Ontology_Annotations The file `ATH_GO_GOSLIM.txt` might be of interest for you. It contains ...
written 20 days ago by massa.kassa.sc3na150
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Answer: A: Chunk That Fasta?
... Hi, try this [link](https://stackoverflow.com/questions/312443/how-do-you-split-a-list-into-evenly-sized-chunks). (just load the genome as string and pass with to one of the implementations of `chunker` from the link). If you have **very** low RAM or **very** long genome then you could do something ...
written 21 days ago by massa.kassa.sc3na150
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Answer: A: Recover from protein ID the corresponding nucleotide ID .
... Hi, the most easy way I've found to obtain the nucleotide sequence for the protein with its ID is to go for efetch (from Entrez Direct). efetch -db protein -id YP_009344822.1 -format fasta_cds_na >lcl|NC_033554.1_cds_YP_009344822.1_1 [gene=TrAP] [locus_tag=BZL59_gp4] [db_xref=GeneID:309 ...
written 21 days ago by massa.kassa.sc3na150
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Comment: C: Comparing two columns of one file with two columns of another file, print all th
... Hi, I've tested it with the provided data, is it possible that you have some 'NaN' value somewhere (that's float in python pandas)? Also you can add if not isinstance(longkey, str): return '' But I thing that you should pre-process your data. ...
written 21 days ago by massa.kassa.sc3na150

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Scholar 1 day ago, created an answer that has been accepted. For C: BLAST using Biopython
Scholar 20 days 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

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