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Behaviour of the 'nmatch' thresshold in seqinr's function dotPlot() - R
written by Gabriel •When comparing two sequences by means of a dot plot, the **seqinr** package provides the **dotPlot()** function, that compares two sequences by marking with a …
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Calculate melting temperature for BLAST output (DNA duplexes with mismatches and gaps)
written by stoptime_armstrong •I know there are a lot of methods to estimate the Tm of a sequence with mismatches and gaps. I've been using biopython and getting …
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Comparing two sets of 16s sequences to identify any identicle (within 97%) sequences
written by robert.murphy •I have two sets of 16s sequences and want to see if there are any sequences within 97% similarity. Blastn uses local alignment and I …
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Probability of finding a common sub-sequence of at least 'k' nucleotides between two sequences.
written by Carlo YagueSuppose we have two random sequences A and B of **L nucleotide** each. What is the probability to observe a common substring (kmer) of at …
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A tool to align two assembled sequences
written by User000<p>Hello,</p> <p>I have two assembled sequences and I would like to compare them. I am interested to get to know the similarity % between them, …
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Appropriate Alignment Algorithm
written by Maria •<p>Hi, I want to compare 2 genomic sequences, one is the reference (r) the other is the query, the reference is composed of 2 genes …
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Global Sequence Alignment
written by behrang •<p>can any body help me with the following problem?</p> <p>For a parameter k, compute the global alignment between two strings, subject to the constraint that …
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Semi Global Alignment
written by Maria •<p>hello, </p> <p>I'm trying to write a code to algin 2 sequences where gaps are for free in the beginning and the end of the …
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R/Biostring: Print Sequence Alignment To File
written by Emempe •<p>I do a simple pairwise DNA sequence alignment with pairwiseAlignment from the Biostrings package in Bioconductor:</p> <pre><code>library('Biostrings') seq1 = 'ATGCTA' seq2 = 'ATGTA' pairwiseAlignment(pattern = …
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Semi-Global Alignment Tool?
written by Ryan Thompson<p>Does anyone know of any general-purpose semiglobal alignment tools? Something like BLAST for semiglobal alignments instead of local alignments. </p> <p>A semiglobal alignment is like …
Is this your homework? hint: look at Smith and Waterman algorithm
do you think you are very smart? If you are, you will implement or copycat if less so the Needleman-Wunsch algorithm. Please remeber: We do not take, repeat do not take, your course assignments.