Moderator: a.zielezinski

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a.zielezinski7.4k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: Trying to reproduce mirbase results locally with BLAST
... blastn -query [file] -db [file] -task blastn-short -word_size 4 -penalty -4 -reward 5 -dust no -soft_masking false -num_alignments 100 ...
written 2 days ago by a.zielezinski7.4k
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Comment: C: Find all genes having ATTAGTTAA in their 3'UTRs
... You can download 3'UTR sequences of all genes from [flybase FTP server][1]. For example, to download all 3'UTRs from D. melanogaster click [on this link][2]. [1]: ftp://ftp.flybase.net/releases/ [2]: ftp://ftp.flybase.net/releases/FB2017_05/dmel_r6.18/fasta/dmel-all-three_prime_UTR-r6.18.fasta ...
written 7 days ago by a.zielezinski7.4k
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Comment: C: How do I generate all possible Newick Tree permutations for a set of species giv
... The "ideal output" in your question includes polytomies. Take a look at this answer: [https://stackoverflow.com/questions/17242117/what-python-code-generates-all-possible-groupings-trees-for-binary-operators][1]. [1]: https://stackoverflow.com/questions/17242117/what-python-code-generates-all-po ...
written 6 weeks ago by a.zielezinski7.4k
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Comment: C: Bootstrapping of unaligned sequeces
... If your alignment-free approach is based on k-mers you can resample the original k-mers with replacement. ...
written 6 weeks ago by a.zielezinski7.4k
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Comment: C: RunningTBLASTN many times with python
... Change the line: cmd = "tblastn -query conSeqfile -db db -out out_blast -outfmt 6 -evalue 0.00001" into this: cmd = "tblastn -query {} -db {} -out {} -outfmt 6 -evalue 0.00001".format(conSeqfile, db, out_blast) ...
written 6 weeks ago by a.zielezinski7.4k
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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 10 weeks ago by a.zielezinski7.4k
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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 11 weeks ago by a.zielezinski7.4k
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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 11 weeks ago by a.zielezinski7.4k
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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 11 weeks ago by a.zielezinski7.4k
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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 11 weeks ago by a.zielezinski7.4k

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Commentator 2 days ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
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