User: tamerg

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tamerg80
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Posts by tamerg

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Mismatch in probe ids
... It looks to me those identifers belongs to diferent Affimetrix probe ids. I don't know how you can solve with **hugene10sttranscriptcluster.db** package but alternatively you can try the [biobtreeR][1] package for these mappings. Following example query, maps probe ids you mentioned to the ensembl g ...
written 5 months ago by tamerg80
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Comment: C: Map Drosophila gene IDs to their Human and Mouse homologs
... Depending on which gene ID you mean, have a look at this R package https://bioconductor.org/packages/3.11/bioc/html/biobtreeR.html. It is straightforward once you read the users guide. Let me know if you have questions. ...
written 7 months ago by tamerg80
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Answer: A: Custom substitution matrix in biopython pairwise2 aligner
... how about trying somethig like this import Bio from Bio import pairwise2 from Bio.pairwise2 import format_alignment seq1 = 'AGTCGATCATCGGA' seq2 = 'ATTAGATCATCGGGGA' match_dic = {} match_dic[('A', 'A')] = 2 match_dic[('A', 'C')] = -1 match_dic[('A' ...
written 7 months ago by tamerg80
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Answer: A: Multiple sequence alignment clean-up
... Hi, try with the following way it should keep the duplicates. import sys from Bio import SeqIO def sequence_cleaner(fasta_file, min_length=0, por_n=100): # Create array to add the sequences sequences = [] # Using the Biopython fasta parse we can re ...
written 7 months ago by tamerg80
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Answer: A: Parsing SwissProt sequences from the net
... Hi, It seems that problem is not on your side. As of latest Biopython 1.76, Biopython hasn't applied data format changes [announced][1] by Uniprot. I have seen some implementation in Biopython repository but not a release includes those changes. You may think to try their development version or sk ...
written 7 months ago by tamerg80
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Comment: C: Sequence Pair Alignment in Python. Local and Global Sequence Alignment.
... No problem. I updated my answer with some additional detail of your code. ...
written 7 months ago by tamerg80
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Comment: C: Sequence Pair Alignment in Python. Local and Global Sequence Alignment.
... All right you created the scoring matrix with your `needleman_Wunsch` function and you get the optimal score. But following lines are not needed `res` variable is not matrix just the score # o resto dá erro: S = res[0] # IndexError: invalid index to scalar variable. T = res[1] If you w ...
written 7 months ago by tamerg80
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Answer: C: Genes Symbol Conversion not in biomaRt
... For alternative to the biomaRt and Org.Hs.eg.db check out the [biobtree][1]. It resolved all the genes you mentioned except AC093375.1 which doesn't seem to belong to an ensembl ID. [1]: https://github.com/tamerh/biobtree ...
written 7 months ago by tamerg80
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Answer: A: Gene Id Conversion Tool
... [biobtree][1] is also a strong alternative tool for simple or advanced identifiers mapping and data retrieval for small or large datasets with R/Python packages. [1]: https://github.com/tamerh/biobtree ...
written 9 months ago by tamerg80
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Answer: A: Classify gene ontology (GO) enrichment terms
... As a database you can check out the [biobtree][1] with its R/Python packages based on Ensembl or Uniprot GO terms. Following are some queries in R related to your cases. 1- Filter the genes with immune response bbMapping("Malt1,Ccl2,CCL26",'filter(ensembl.genome=="homo_sapiens").map(go).filter(g ...
written 10 months ago by tamerg80

Latest awards to tamerg

Scholar 7 months ago, created an answer that has been accepted. For A: Multiple sequence alignment clean-up
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Custom substitution matrix in biopython pairwise2 aligner
Scholar 7 months ago, created an answer that has been accepted. For A: Multiple sequence alignment clean-up
Supporter 13 months ago, voted at least 25 times.

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