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This package implements pairwise sequence alignment using a dynamic
programming algorithm.

This provides functions to get global and local alignments between two
sequences.  A global alignment finds the best concordance between all
characters in two sequences.  A local alignment finds just the
subsequences that align the best.

When doing alignments, you can specify the match score and gap
penalties.  The match score indicates the compatibility between an(more...)

src/f/a/fastools-0.9.0/fastools/fastools.py   fastools(Download)
import itertools
import Levenshtein
from Bio import Seq, SeqIO, Entrez, pairwise2, Restriction
from Bio.Alphabet import IUPAC
from Bio.SeqRecord import SeqRecord

src/s/e/seqmagick-0.5.0/seqmagick/subcommands/primer_trim.py   seqmagick(Download)
import sys
 
from Bio import Alphabet, SeqIO, pairwise2
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq

src/s/e/seqmagick-HEAD/seqmagick/subcommands/primer_trim.py   seqmagick(Download)
import sys
 
from Bio import Alphabet, SeqIO, pairwise2
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq

src/b/c/bcbb-HEAD/align/adaptor_trim.py   bcbb(Download)
from optparse import OptionParser
 
from Bio import pairwise2
from Bio.Seq import Seq
from Bio import SeqIO

src/m/g/mgtaxa-HEAD/MGT/Proj/CrisprApp.py   mgtaxa(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature,FeatureLocation
from Bio import pairwise2
from Bio.Blast import NCBIXML
 

src/p/y/pytools-HEAD/seqtools.py   pytools(Download)
from Bio.SeqRecord  import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio            import pairwise2
 
import numpy as np

src/c/o/ContactVis-0.1.5/contactvis/plot_contact_map.py   ContactVis(Download)
 
import Bio.PDB
from Bio import pairwise2
 
import numpy as np

src/b/c/bcbb-HEAD/nextgen/scripts/barcode_sort_trim.py   bcbb(Download)
from optparse import OptionParser
 
from Bio import pairwise2
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 

src/b/c/bcbio-nextgen-0.7.8/scripts/barcode_sort_trim.py   bcbio-nextgen(Download)
from optparse import OptionParser
 
from Bio import pairwise2
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 

src/p/r/ProDy-1.5.1/prody/proteins/compare.py   ProDy(Download)
        except ImportError:
            try:
                from Bio import pairwise2
            except ImportError:
                raise ImportError('pairwise2 module could not be imported. '

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