Moderator: a.zielezinski

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a.zielezinski6.6k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Yes, I can also rewrite the code for you to check whether biopython's id contains your query id. In this way, you wouldn't have to change the code anytime you look for P01731 or CD4_HUMAN. The script would be universal - it will work on any sequences (e.g. from different databases) without changing ...
written 20 hours ago by a.zielezinski6.6k
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Do you mean both sequence records or both ids? ...
written 1 day ago by a.zielezinski6.6k
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... This is because biopython sees id as `sp|P01730|CD4_HUMAN`, rather than `P01730`. I fixed it and updated my answer. ...
written 1 day ago by a.zielezinski6.6k
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Comment: C: Using Biopython to search a fasta file for specific uniprots
... Try to create a small fasta file with id P01730 and then check the script on that file. ...
written 1 day ago by a.zielezinski6.6k
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Answer: A: Using Biopython to search a fasta file for specific uniprots
... This should do the job: from Bio import SeqIO myuniprots = ['P01730', 'P01731'] for record in SeqIO.parse("CD4.fasta", "fasta"): id = record.id.split('|')[1] if '|' in record.id else record.id if id in myuniprots: print("%s %s %i" % (record.id, record.seq, le ...
written 1 day ago by a.zielezinski6.6k
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Comment: C: How to determine if a sequence is nonsatellite sequence?
... To find out, scan your sequence with [RepeatMasker Web Server][1]. [1]: http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker ...
written 1 day ago by a.zielezinski6.6k
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Answer: A: A code for splitting FASTA file, No output is written for the file
... I followed the logic of your script and tweaked it a little. Now, the script should do what you wanted. However, I just want to let you know that there are other (more efficient and less complicated) - ways to implement this task in Python. file_open = open("sequence.txt","r") MAX_FILES = ...
written 4 days ago by a.zielezinski6.6k
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Answer: A: How to get total count of organisms with whole genome sequenced
... See [The Genomes OnLine Database (GOLD)][1]. It is a web-based resource for comprehensive information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. The database provides all the statistics for various statuses of sequencing projects, such as: ...
written 6 days ago by a.zielezinski6.6k
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Answer: A: How to calculate log scores from an alignment?
... **1.** `n(C&G)` is the number of times when C is substituted with G (or G with C). For example, In the first column of the alignment you have 4 C and 2 G, which gives you 4*2 = 8 C <-> G subsitutions. In the second column, you have 3 * 2 = 6 C<>G substitutions, In the third column, ...
written 14 days ago by a.zielezinski6.6k
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Comment: C: Can anybody explain what this statement says?
... They look suspicious. I'm not familiar with the software. It will be a lot easier to understand an output if you use small k-mers (for example = 1 or 2). ...
written 14 days ago by a.zielezinski6.6k

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