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Showing posts with the label Bioinformatics

Biopython Alignio Valueerror Says Strings Must Be Same Length?

Input fasta-format text file: http://www.jcvi.org/cgi-bin/tigrfams/DownloadFile.cgi?file=/opt/www/w… Read more Biopython Alignio Valueerror Says Strings Must Be Same Length?

Finding Common Id's (intersection) In Two Dictionaries

I wrote a piece of code that is supposed to find common intersecting ID's in line[1] in two dif… Read more Finding Common Id's (intersection) In Two Dictionaries

Python: Multiple Consensus Sequences

starting from a list of dna sequences, I must have in return all the possible consensus (the result… Read more Python: Multiple Consensus Sequences

Traceback In Smith-wateman Algorithm With Affine Gap Penalty

I'm trying to implement the Smith-Waterman algorithm for local sequence alignment using the aff… Read more Traceback In Smith-wateman Algorithm With Affine Gap Penalty

Search For Motifs With Degenerate Positions

I have a 15-mer nucleotide motif that uses degenerate nucleotide sequences. Example: ATNTTRTCNGGHGC… Read more Search For Motifs With Degenerate Positions

Can I Use K-means Algorithm On A String?

I am working on a python project where I study RNA structure evolution (represented as a string for… Read more Can I Use K-means Algorithm On A String?

Traceback In Smith-Wateman Algorithm With Affine Gap Penalty

I'm trying to implement the Smith-Waterman algorithm for local sequence alignment using the aff… Read more Traceback In Smith-Wateman Algorithm With Affine Gap Penalty

Traceback In Smith-Wateman Algorithm With Affine Gap Penalty

I'm trying to implement the Smith-Waterman algorithm for local sequence alignment using the aff… Read more Traceback In Smith-Wateman Algorithm With Affine Gap Penalty