Moderator: a.zielezinski

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a.zielezinski7.3k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: Convert sequence file to fasta format using python
... Or even simpler: import sys for c, l in enumerate(sys.stdin, start=1): sys.stdout.write(">%d\n%s\n" % (c, l)) ...
written 11 days ago by a.zielezinski7.3k
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Comment: C: how to get database of plants in FASTA format from uniprot
... Sure! If I answered your question, please mark my post as accepted by clicking on the thick (check sign) icon. ...
written 19 days ago by a.zielezinski7.3k
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Answer: A: how to combine multiple fasta file into a larger fasta file
... As genomax said, this task is too simple for Python. However, if you still insist on solving this with Python, here's the solution: import os DIR = 'fasta_files/' oh = open('one_fasta_file.fasta', 'w') for f in os.listdir(DIR): fh = open(os.path.join(DIR, f)) ...
written 22 days ago by a.zielezinski7.3k
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Comment: C: Batch PFam search
... Download PfamScan from [ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/][1] and use it from the command-line. [1]: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ ...
written 23 days ago by a.zielezinski7.3k
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Answer: A: how to get database of plants in FASTA format from uniprot
... 1. Go to UniProt website 2. Search for: `taxonomy:viridiplantae` 3. Click on the `Download` button: - Check `Download all` - Select **Format:** `FASTA` - Check `Compressed` - Click **GO**. ...
written 23 days ago by a.zielezinski7.3k
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Answer: A: reverse_complement on mutated sequence Biopython
... The method `reverse_complement()` executed on mutable sequence, reverse the sequence in place and returns `None` value, so you shouldn't assign it to a variable. For example: from Bio.Seq import Seq seq = Seq("ACGTTGCAC") mutseq = seq.tomutable() mutseq.reverse_complement() ...
written 4 weeks ago by a.zielezinski7.3k
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Answer: A: Parse fasta header with regex in python
... This should do the work: from Bio import SeqIO infile = "seq.fa" ...
written 4 weeks ago by a.zielezinski7.3k
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Answer: A: how to converting hordeum vulgare gene IDs (e.g. HORVU1Hr1G001920.3) to NCBI gen
... Files mapping HORVU* identifiers to UniProt/RefSeq accession numbers: [ftp://ftp.ensemblgenomes.org/pub/release-36/plants/tsv/hordeum_vulgare/][1] or alternatively, you can use [BioMart tool in Ensembl Plants][2] to translate identifiers. [1]: ftp://ftp.ensemblgenomes.org/pub/release-36/plants ...
written 5 weeks ago by a.zielezinski7.3k
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Answer: A: Intall local BLAST in Ubuntu
... sudo apt-get install ncbi-blast+ ...
written 6 weeks ago by a.zielezinski7.3k
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Comment: C: how to align lists of words using biopython pairwise2
... Thanks for posting this info. Good to know that. ...
written 7 weeks ago by a.zielezinski7.3k

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