Sequence Similarity Search Demo¶

This demo filters PDB chains by sequence similarity using RCSB PDB webservices.

Imports¶

In [1]:

from pyspark import SparkConf, SparkContext
from mmtfPyspark.webfilters import SequenceSimilarity
from mmtfPyspark.mappers import StructureToPolymerChains
from mmtfPyspark.io import mmtfReader

Configure Spark Context¶

In [2]:

conf = SparkConf().setMaster("local[*]") \
                  .setAppName("SequenceSimilaritySearchDemo")
sc = SparkContext(conf = conf)

Read PDB in MMTF format, split into polymer chain, search by sequence similarity, and print sequence found¶

In [6]:

path = "../../resources/mmtf_reduced_sample/"

pdb = mmtfReader.read_sequence_file(path, sc) \
                .flatMap(StructureToPolymerChains()) \
                .filter(SequenceSimilarity(sequence="NLVQFGVMIEKMTGKSALQYNDYGCYCGIGGSHWPVDQ",\
                                           searchTool=SequenceSimilarity.BLAST, \
                                           eValueCutoff=0.001, \
                                           sequenceIdentityCutoff=40, \
                                           maskLowComplexity=True)) \
                .collect()

for pdbId, structure in pdb:
        print(f"{pdbId} :     {structure.entity_list[0]['sequence']}")

2H4C.A :     NFFQFAEMIVKMTGKEAVHSYAIYGCYCGWGGQGKPQDATDRCCFVHDCCYGTVNDCNPKMATYSYSFENGDIVCGDNNLCLKTVCECDRAAAICLGQNVNTYDKNYENYAISHCTEESEQC
2H4C.C :     NFFQFAEMIVKMTGKEAVHSYAIYGCYCGWGGQGKPQDATDRCCFVHDCCYGTVNDCNPKMATYSYSFENGDIVCGDNNLCLKTVCECDRAAAICLGQNVNTYDKNYENYAISHCTEESEQC
2H4C.E :     NFFQFAEMIVKMTGKEAVHSYAIYGCYCGWGGQGKPQDATDRCCFVHDCCYGTVNDCNPKMATYSYSFENGDIVCGDNNLCLKTVCECDRAAAICLGQNVNTYDKNYENYAISHCTEESEQC
2H4C.G :     NFFQFAEMIVKMTGKEAVHSYAIYGCYCGWGGQGKPQDATDRCCFVHDCCYGTVNDCNPKMATYSYSFENGDIVCGDNNLCLKTVCECDRAAAICLGQNVNTYDKNYENYAISHCTEESEQC
1GP7.A :     MNPAHLLVLSAVCVSLLGASSIPPQPLHLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC
1GP7.B :     MNPAHLLVLSAVCVSLLGASSIPPQPLHLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC
1GP7.C :     MNPAHLLVLSAVCVSLLGASSIPPQPLHLIQFGNMIQCTVPGFLSWIKYADYGCYCGAGGSGTPVDKLDRCCQVHDNCYTQAQKLPACSSIMDSPYVKIYSYDCSERTVTCKADNDECAAFICNCDRVAAHCFAASPYNNNNYNIDTTTRC
3V9M.A :     NLIQFGNMIQCANKGSRPSLDYADYGCYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKCFAKAPYKKENYNIDTKKRCK
3V9M.B :     NLIQFGNMIQCANKGSRPSLDYADYGCYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKCFAKAPYKKENYNIDTKKRCK
3VC0.A :     NLVQFGKMIECAIRNRRPALDFMNYGCYCGKGGSGTPVDDLDRCCQVHDECYAEAEKHGCYPSLTTYTWECRQVGPYCNSKTQCEVFVCACDFAAAKCFAQEDYNPAHSNINTGERCK
1VAP.A :     NLFQFEKLIKKMTGKSGMLWYSAYGCYCGWGGQGRPKDATDRCCFVHDCCYGKVTGCNPKMDIYTYSVDNGNIVCGGTNPCKKQICECDRAAAICFRDNLKTYDSKTYWKYPKKNCKEESEPC
1VAP.B :     NLFQFEKLIKKMTGKSGMLWYSAYGCYCGWGGQGRPKDATDRCCFVHDCCYGKVTGCNPKMDIYTYSVDNGNIVCGGTNPCKKQICECDRAAAICFRDNLKTYDSKTYWKYPKKNCKEESEPC
1VIP.A :     NLFQFAEMIVKMTGKNPLSSYSDYGCYCGWGGKGKPQDATDRCCFVHDCCYEKVKSCKPKLSLYSYSFQNGGIVCGDNHSCKRAVCECDRVAATCFRDNLNTYDKKYHNYPPSQCTGTEQC

Terminate Spark Context¶

In [7]:

sc.stop()

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