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test_GenBank.py
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test_GenBank.py
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# Copyright 2001-2004 by Brad Chapman. All rights reserved.
# Revisions copyright 2007-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2013 by Kai Blin. All rights reserved.
# Revisions copyright 2015-2016 by Peter Cock.
# Revisions copyright 2019 by Sergio Valqui.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for the GenBank module."""
import os
import sys
import unittest
import warnings
from datetime import datetime
from io import StringIO
from Bio import BiopythonWarning
from Bio import BiopythonParserWarning
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq, UndefinedSequenceError
# GenBank stuff to test:
from Bio import GenBank
class TestBasics(unittest.TestCase):
def do_comparison(self, good_record, test_record):
"""Compare two records to see if they are the same.
This compares the two GenBank records line by line.
"""
good_handle = StringIO(good_record)
test_handle = StringIO(test_record)
while True:
good_line = good_handle.readline()
test_line = test_handle.readline()
if not good_line and not test_line:
break
self.assertTrue(good_line, "Extra info in Test: %r" % test_line)
self.assertTrue(test_line, "Extra info in Expected: %r" % good_line)
test_normalized = " ".join(x for x in test_line.split() if x)
good_normalized = " ".join(x for x in good_line.split() if x)
self.assertEqual(test_normalized, good_normalized)
def test_write_format(self):
"""Test writing to the difference formats."""
# We only test writing on a subset of the examples:
filenames = [
"noref.gb",
"cor6_6.gb",
"iro.gb",
"pri1.gb",
"arab1.gb",
"extra_keywords.gb",
"one_of.gb",
"origin_line.gb",
]
# don't test writing on protein_refseq, since it is horribly nasty
# don't test writing on the CONTIG refseq, because the wrapping of
# locations won't work exactly
# don't test writing on blank_seq because it lacks a sequence type
# don't test dbsource_wrap because it is a junky RefSeq file
record_parser = GenBank.RecordParser(debug_level=0)
for filename in filenames:
path = os.path.join("GenBank", filename)
with open(path) as cur_handle, open(path) as compare_handle:
iterator = GenBank.Iterator(cur_handle, record_parser)
compare_iterator = GenBank.Iterator(compare_handle)
while True:
cur_rec = next(iterator)
compare_record = next(compare_iterator)
if cur_rec is None or compare_record is None:
break
output_record = str(cur_rec) + "\n"
self.do_comparison(compare_record, output_record)
def test_cleaning_features(self):
"""Test the ability to clean up feature values."""
gb_parser = GenBank.FeatureParser(
feature_cleaner=GenBank.utils.FeatureValueCleaner()
)
path = "GenBank/arab1.gb"
with open(path) as handle:
iterator = GenBank.Iterator(handle, gb_parser)
first_record = next(iterator)
# test for cleaning of translation
translation_feature = first_record.features[1]
test_trans = translation_feature.qualifiers["translation"][0]
self.assertNotIn(" ", test_trans, "Did not clean spaces out of the translation")
self.assertNotIn(
"\012", test_trans, "Did not clean newlines out of the translation"
)
def test_ensembl_locus(self):
"""Test the ENSEMBL locus line."""
line = "LOCUS HG531_PATCH 1000000 bp DNA HTG 18-JUN-2011\n"
s = GenBank.Scanner.GenBankScanner()
c = GenBank._FeatureConsumer(True)
s._feed_first_line(c, line)
self.assertEqual(c.data.name, "HG531_PATCH")
self.assertEqual(c._expected_size, 1000000)
line = "LOCUS HG531_PATCH 759984 bp DNA HTG 18-JUN-2011\n"
s = GenBank.Scanner.GenBankScanner()
c = GenBank._FeatureConsumer(True)
s._feed_first_line(c, line)
self.assertEqual(c.data.name, "HG531_PATCH")
self.assertEqual(c._expected_size, 759984)
line = "LOCUS HG506_HG1000_1_PATCH 814959 bp DNA HTG 18-JUN-2011\n"
s = GenBank.Scanner.GenBankScanner()
c = GenBank._FeatureConsumer(True)
s._feed_first_line(c, line)
self.assertEqual(c.data.name, "HG506_HG1000_1_PATCH")
self.assertEqual(c._expected_size, 814959)
line = "LOCUS HG506_HG1000_1_PATCH 1219964 bp DNA HTG 18-JUN-2011\n"
s = GenBank.Scanner.GenBankScanner()
c = GenBank._FeatureConsumer(True)
s._feed_first_line(c, line)
self.assertEqual(c.data.name, "HG506_HG1000_1_PATCH")
self.assertEqual(c._expected_size, 1219964)
class TestRecordParser(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.rec_parser = GenBank.RecordParser(debug_level=0)
def perform_record_parser_test(
self,
record,
length,
locus,
definition,
accession,
titles,
features,
tls=None,
tsa=None,
):
self.assertEqual(len(record.sequence), length)
self.assertEqual(record.locus, locus)
self.assertEqual(record.definition, definition)
self.assertEqual(record.accession, accession)
self.assertEqual(
tuple(reference.title for reference in record.references), titles
)
self.assertEqual(len(record.features), len(features))
for feature1, feature2 in zip(record.features, features):
self.assertEqual(feature1.key, feature2[0])
self.assertEqual(feature1.location, feature2[1])
self.assertEqual(len(feature1.qualifiers), len(feature2[2]))
for qualifier, (key, value) in zip(feature1.qualifiers, feature2[2]):
self.assertEqual(qualifier.key, key)
self.assertEqual(qualifier.value, value)
if tls:
self.assertEqual(tls, record.tls)
if tsa:
self.assertEqual(tsa, record.tsa)
def test_record_parser_01(self):
path = "GenBank/noref.gb"
with open(path) as handle:
records = GenBank.Iterator(handle, self.rec_parser)
record = next(records)
length = 1622
locus = "NM_006141"
definition = (
"Homo sapiens dynein, cytoplasmic, light intermediate polypeptide 2 "
"(DNCLI2), mRNA"
)
accession = ["NM_006141"]
titles = ()
features = [
(
"source",
"1..1622",
(
("/organism=", '"Homo sapiens"'),
("/db_xref=", '"taxon:9606"'),
("/map=", '"16"'),
),
),
(
"gene",
"1..1622",
(
("/gene=", '"DNCLI2"'),
("/note=", '"LIC2"'),
("/db_xref=", '"LocusID:1783"'),
),
),
(
"CDS",
"7..1485",
(
("/gene=", '"DNCLI2"'),
(
"/note=",
'"similar to R. norvegicus and G. gallus dynein light '
"intermediate chain 2, Swiss-Prot Accession Numbers Q62698 and "
'Q90828, respectively"',
),
("/codon_start=", "1"),
("/db_xref=", '"LocusID:1783"'),
(
"/product=",
'"dynein, cytoplasmic, light intermediate polypeptide 2"',
),
("/protein_id=", '"NP_006132.1"'),
("/db_xref=", '"GI:5453634"'),
(
"/translation=",
'"MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVSTRARSKLPSGKNILVFG'
"EDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHTRCNVWILDGDLYHKGLLKFAV"
"SAESLPETLVIFVADMSRPWTVMESLQKWASVLREHIDKMKIPPEKMRELERKFVKDFQDYM"
"EPEEGCQGSPQRRGPLTSGSDEENVALPLGDNVLTHNLGIPVLVVCTKCDAVSVLEKEHDYR"
"DEHLDFIQSHLRRFCLQYGAALIYTSVKEEKNLDLLYKYIVHKTYGFHFTTPALVVEKDAVF"
"IPAGWDNEKKIAILHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQVFLMKQQSLLA"
"KQPATPTRASESPARGPSGSPRTQGRGGPASVPSSSPGTSVKKPDPNIKNNAASEGVLASFF"
'NSLLSKKTGSPGSPGAGGVQSTAKKSGQKTVLSNVQEELDRMTRKPDSMVTNSSTENEA"',
),
),
),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
def test_record_parser_02(self):
path = "GenBank/cor6_6.gb"
with open(path) as handle:
records = GenBank.Iterator(handle, self.rec_parser)
record = next(records)
length = 513
locus = "ATCOR66M"
definition = "A.thaliana cor6.6 mRNA"
accession = ["X55053"]
titles = (
"Direct Submission",
"cDNA sequence analysis and expression of two cold-regulated genes of "
"Arabidopsis thaliana",
)
features = [
(
"source",
"1..513",
(
("/organism=", '"Arabidopsis thaliana"'),
("/strain=", '"Columbia"'),
("/db_xref=", '"taxon:3702"'),
),
),
("gene", "50..250", (("/gene=", '"cor6.6"'),)),
(
"CDS",
"50..250",
(
("/gene=", '"cor6.6"'),
("/note=", '"cold regulated"'),
("/codon_start=", "1"),
("/protein_id=", '"CAA38894.1"'),
("/db_xref=", '"GI:16230"'),
("/db_xref=", '"SWISS-PROT:P31169"'),
(
"/translation=",
'"MSETNKNAFQAGQAAGKAEEKSNVLLDKAKDAAAAAGASAQQAGKSISDAAVGGVNF'
'VKDKTGLNK"',
),
),
),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
record = next(records)
length = 880
locus = "ATKIN2"
definition = "A.thaliana kin2 gene"
accession = ["X62281"]
titles = (
"Direct Submission",
"Structure and expression of kin2, one of two cold- and ABA-induced "
"genes of Arabidopsis thaliana",
)
features = [
(
"source",
"1..880",
(
("/organism=", '"Arabidopsis thaliana"'),
("/strain=", '"ssp. L. Heynh, Colombia"'),
("/db_xref=", '"taxon:3702"'),
),
),
("TATA_signal", "9..20", ()),
("exon", "44..160", (("/gene=", '"kin2"'), ("/number=", "1"))),
("prim_transcript", "44..>579", (("/gene=", '"kin2"'),)),
("mRNA", "join(44..160,320..390,504..>579)", (("/gene=", '"kin2"'),)),
("gene", "44..579", (("/gene=", '"kin2"'),)),
(
"CDS",
"join(104..160,320..390,504..579)",
(
("/gene=", '"kin2"'),
("/codon_start=", "1"),
("/protein_id=", '"CAA44171.1"'),
("/db_xref=", '"GI:16354"'),
("/db_xref=", '"SWISS-PROT:P31169"'),
(
"/translation=",
'"MSETNKNAFQAGQAAGKAERRRAMFCWTRPRMLLLQLELPRNRAGKSISDAAVGGVN'
'FVKDKTGLNK"',
),
),
),
("intron", "161..319", (("/gene=", '"kin2"'), ("/number=", "1"))),
("exon", "320..390", (("/gene=", '"kin2"'), ("/number=", "2"))),
("intron", "391..503", (("/gene=", '"kin2"'), ("/number=", "2"))),
("exon", "504..>579", (("/gene=", '"kin2"'), ("/number=", "3"))),
("polyA_signal", "620..625", ()),
("polyA_signal", "641..646", ()),
("polyA_site", "785", ()),
("polyA_site", "800", ()),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
record = next(records)
length = 441
locus = "BNAKINI"
definition = "Rapeseed Kin1 protein (kin1) mRNA, complete cds"
accession = ["M81224"]
titles = ("Nucleotide sequence of a winter B. napus Kin 1 cDNA",)
features = [
(
"source",
"1..441",
(
("/organism=", '"Brassica napus"'),
("/cultivar=", '"Jet neuf"'),
("/db_xref=", '"taxon:3708"'),
("/dev_stage=", '"cold induced"'),
("/tissue_type=", '"leaf"'),
),
),
("gene", "34..300", (("/gene=", '"kin1"'),)),
(
"CDS",
"34..231",
(
("/gene=", '"kin1"'),
("/codon_start=", "1"),
("/evidence=", "experimental"),
("/protein_id=", '"AAA32993.1"'),
("/db_xref=", '"GI:167146"'),
(
"/translation=",
'"MADNKQSFQAGQASGRAEEKGNVLMDKVKDAATAAGASAQTAGQKITEAAGGAVNLV'
'KEKTGMNK"',
),
),
),
(
"polyA_signal",
"241..247",
(("/gene=", '"kin1"'), ("/note=", '"putative"')),
),
(
"polyA_signal",
"294..300",
(("/gene=", '"kin1"'), ("/note=", '"putative"')),
),
("polyA_site", "441", (("/gene=", '"kin1"'),)),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
record = next(records)
length = 206
locus = "ARU237582"
definition = "Armoracia rusticana csp14 gene (partial), exons 2-3"
accession = ["AJ237582"]
titles = ("", "Direct Submission")
features = [
(
"source",
"1..206",
(
("/organism=", '"Armoracia rusticana"'),
("/db_xref=", '"taxon:3704"'),
("/country=", '"Russia:Bashkortostan"'),
),
),
("mRNA", "join(<1..48,143..>206)", (("/gene=", '"csp14"'),)),
("exon", "1..48", (("/gene=", '"csp14"'), ("/number=", "2"))),
("gene", "1..206", (("/gene=", '"csp14"'),)),
(
"CDS",
"join(<1..48,143..>206)",
(
("/gene=", '"csp14"'),
("/codon_start=", "2"),
("/product=", '"cold shock protein"'),
("/protein_id=", '"CAB39890.1"'),
("/db_xref=", '"GI:4538893"'),
("/translation=", '"DKAKDAAAAAGASAQQAGKNISDAAAGGVNFVKEKTG"'),
),
),
("intron", "49..142", (("/gene=", '"csp14"'), ("/number=", "2"))),
("exon", "143..206", (("/gene=", '"csp14"'), ("/number=", "3"))),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
record = next(records)
length = 282
locus = "BRRBIF72"
definition = "Brassica rapa (clone bif72) kin mRNA, complete cds"
accession = ["L31939"]
titles = ("Nucleotide sequences of kin gene in chinese cabbage",)
features = [
(
"source",
"1..282",
(
("/organism=", '"Brassica rapa"'),
("/db_xref=", '"taxon:3711"'),
("/dev_stage=", '"flower"'),
),
),
("gene", "24..221", (("/gene=", '"kin"'),)),
(
"CDS",
"24..221",
(
("/gene=", '"kin"'),
("/codon_start=", "1"),
("/protein_id=", '"AAA91051.1"'),
("/db_xref=", '"GI:1209262"'),
(
"/translation=",
'"MADNKQSFQAGQAAGRAEEKGNVLLMDKVKDAATAAGALQTAGQKITEAAGGAVNLV'
'KEKTGMNK"',
),
),
),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
record = next(records)
length = 497
locus = "AF297471"
definition = "Brassica napus BN28a (BN28a) gene, complete cds"
accession = ["AF297471"]
titles = (
"BN28a, a low temperature-induced gene of Brassica napus",
"Direct Submission",
)
features = [
(
"source",
"1..497",
(
("/organism=", '"Brassica napus"'),
("/cultivar=", '"Cascade"'),
("/db_xref=", '"taxon:3708"'),
),
),
(
"mRNA",
"join(<1..54,241..309,423..>497)",
(("/gene=", '"BN28a"'), ("/product=", '"BN28a"')),
),
("gene", "<1..>497", (("/gene=", '"BN28a"'),)),
(
"CDS",
"join(1..54,241..309,423..497)",
(
("/gene=", '"BN28a"'),
(
"/note=",
'"low temperature-induced; similar to Brassica napus Kin1 '
'in Accession Number M81224"',
),
("/codon_start=", "1"),
("/product=", '"BN28a"'),
("/protein_id=", '"AAG13407.1"'),
("/db_xref=", '"GI:10121869"'),
(
"/translation=",
'"MADNKQSFQAGQAAGRAEEKGNVLMDKVKDAATAAGASAQTAGQKITEAAGGAVNLV'
'KEKTGMNK"',
),
),
),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
def test_record_parser_03(self):
path = "GenBank/iro.gb"
with open(path) as handle:
records = GenBank.Iterator(handle, self.rec_parser)
record = next(records)
length = 1326
locus = "IRO125195"
definition = "Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 125195"
accession = ["AL109817"]
titles = (
"The European IMAGE consortium for integrated Molecular analysis "
"of human gene transcripts",
"Direct Submission",
)
features = [
(
"source",
"1..1326",
(
("/organism=", '"Homo sapiens"'),
("/db_xref=", '"taxon:9606"'),
("/chromosome=", '"21"'),
("/clone=", '"IMAGE cDNA clone 125195"'),
("/clone_lib=", '"Soares fetal liver spleen 1NFLS"'),
(
"/note=",
'"contains Alu repeat; '
"likely to be be derived from unprocessed nuclear RNA "
"or genomic DNA; "
"encodes putative exons identical to FTCD; "
"formimino transferase cyclodeaminase; "
"formimino transferase (EC 2.1.2.5) "
'/formimino tetrahydro folate cyclodeaminase (EC 4.3.1.4)"',
),
),
),
("gene", "341..756", (("/gene=", '"FTCD"'),)),
("exon", "341..384", (("/gene=", '"FTCD"'), ("/number=", "1"))),
("intron", "385..617", (("/gene=", '"FTCD"'), ("/number=", "1"))),
("exon", "618..756", (("/gene=", '"FTCD"'), ("/number=", "2"))),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
def test_record_parser_04(self):
path = "GenBank/pri1.gb"
with open(path) as handle:
records = GenBank.Iterator(handle, self.rec_parser)
record = next(records)
length = 741
locus = "HUGLUT1"
definition = "Human fructose transporter (GLUT5) gene, promoter and exon 1"
accession = ["U05344"]
titles = (
"Regulation of expression of the human fructose transporter (GLUT5) by "
"cyclic AMP",
"Direct Submission",
)
features = [
(
"source",
"1..741",
(
("/organism=", '"Homo sapiens"'),
("/db_xref=", '"taxon:9606"'),
("/chromosome=", '"1"'),
("/map=", '"1p31"'),
("/clone=", '"lambda hGT5-157"'),
("/tissue_type=", '"liver"'),
(
"/clone_lib=",
'"partial Hae III/Alu I fetal human liver library in lambda '
'Ch4A of Maniatis"',
),
("/dev_stage=", '"fetal"'),
),
),
("repeat_region", "1..73", (("/rpt_family=", '"Alu"'),)),
("promoter", "1..513", ()),
("5'UTR", "514..609", (("/gene=", '"GLUT5"'),)),
(
"exon",
"514..642",
(
("/gene=", '"GLUT5"'),
("/number=", "1"),
("/product=", '"fructose transporter"'),
),
),
]
self.perform_record_parser_test(
record, length, locus, definition, accession, titles, features
)
def test_record_parser_05(self):
path = "GenBank/arab1.gb"
with open(path) as handle:
records = GenBank.Iterator(handle, self.rec_parser)
record = next(records)
length = 86436
locus = "AC007323"
definition = (
"Genomic sequence for Arabidopsis thaliana BAC T25K16 from chromosome I, "
"complete sequence"
)
accession = ["AC007323"]
titles = (
"Genomic sequence for Arabidopsis thaliana BAC T25K16 from chromosome I",
"Direct Submission",
"Direct Submission",
"Direct Submission",
"Direct Submission",
)
features = [
(
"source",
"1..86436",
(
("/organism=", '"Arabidopsis thaliana"'),
("/db_xref=", '"taxon:3702"'),
("/chromosome=", '"1"'),
("/clone=", '"T25K16"'),
),
),
(
"CDS",
"join(3462..3615,3698..3978,4077..4307,4408..4797,4876..5028,5141..5332)",
(
(
"/note=",
'"containing similarity to NAM-like proteins gi|3695378"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.1"'),
("/protein_id=", '"AAF26460.1"'),
("/db_xref=", '"GI:6715633"'),
(
"/translation=",
'"MEDQVGFGFRPNDEELVGHYLRNKIEGNTSRDVEVAISEVNICSYDPWNLRFQSKYKSRDA'
"MWYFFSRRENNKGNRQSRTTVSGKWKLTGESVEVKDQWGFCSEGFRGKIGHKRVLVFLDGRY"
"PDKTKSDWVIHEFHYDLLPEHQKLCNVTLFRFSSYFRLSLLSPMFYTDELMCLPPEILQRTY"
"VICRLEYKGDDADILSAYAIDPTPAFVPNMTSSAGSVVNQSRQRNSGSYNTYSEYDSANHGQ"
"QFNENSNIMQQQPLQGSFNPLLEYDFANHGGQWLSDYIDLQQQVPYLAPYENESEMIWKHVI"
"EENFEFLVDERTSMQQHYSDHRPKKPVSGVLPDDSSDTETGSMIFEDTSSSTDSVGSSDEPG"
"HTRIDDIPSLNIIEPLHNYKAQEQPKQQSKEKVISSQKSECEWKMAEDSIKIPPSTNTVKQS"
'WIVLENAQWNYLKNMIIGVLLFISVISWIILVG"',
),
),
),
(
"CDS",
"complement(join("
"6617..6953,7266..7351,7464..7603,7916..7998,8087..8166,8273..8368"
"))",
(
("/note=", '"hypothetical protein"'),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.2"'),
("/protein_id=", '"AAF26477.1"'),
("/db_xref=", '"GI:6715650"'),
(
"/translation=",
'"MAASEHRCVGCGFRVKSLFIQYSPGNIRLMKCGNCKEVADEYIECERMVCFNHFLSLFGPK'
"VYRHVLYNAINPATVNIQVKNYFNSTSRCVVGEIHRQTYLKSPELIIDRSLLLRKSDEESSF"
"SDSPVLLSIKVLIGVLSANAAFIISFAIATKGLLNEVSRESLLLQVWEFPMSVIFFVDILLL"
"TSNSMALKGQTFKMFSMQIVFCCCYFGISQCKFVFKPVMTESTMTRCIAVCLIAHLIRFLVG"
'QIFEPTIFLIQIGSLLQYMSYFFRIV"',
),
),
),
(
"CDS",
"complement(11566..12642)",
(
("/note=", '"putative RAP2.8 protein gi|3695373"'),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.3"'),
("/protein_id=", '"AAF26476.1"'),
("/db_xref=", '"GI:6715649"'),
(
"/translation=",
'"MDLSLAPTTTTSSDQEQDRDQELTSNIGASSSSGPSGNNNNLPMMMIPPPEKEHMFDKVVT'
"PSDVGKLNRLVIPKQHAERYFPLDSSNNQNGTLLNFQDRNGKMWRFRYSYWNSSQSYVMTKG"
"WSRFVKEKKLDAGDIVSFQRGIGDESERSKLYIDWRHRPDMSLVQAHQFGNFGFNFNFPTTS"
"QYSNRFHPLPEYNSVPIHRGLNIGNHQRSYYNTQRQEFVGYGYGNLAGRCYYTGSPLDHRNI"
"VGSEPLVIDSVPVVPGRLTPVMLPPLPPPPSTAGKRLRLFGVNMECGNDYNQQEESWLVPRG"
'EIGASSSSSSALRLNLSTDHDDDNDDGDDGDDDQFAKKGKSSLSLNFNP"',
),
),
),
(
"CDS",
"join("
"23221..24174,24244..24357,24412..24664,24743..25137,25226..25445,"
"25527..25711,25783..25905,25994..26478,26564..26730,26814..26983,"
"27074..27235,27320..27415,27505..28133,28314..28507,28592..28782,"
"28862..30013,30112..30518,30604..30781"
")",
(
(
"/note=",
'"similar to UFD1 protein emb|CAB10321.1; similar to ESTs '
'gb|H36434, gb|AI996152.1"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.4"'),
("/protein_id=", '"AAF26461.1"'),
("/db_xref=", '"GI:6715634"'),
(
"/translation=",
'"MVMEDEPREATIKPSYWLDACEDISCDLIDDLVSEFDPSSVAVNESTDENGVINDFFGGID'
"HILDSIKNGGGLPNNGVSDTNSQINEVTVTPQVIAKETVKENGLQKNGGKRDEFSKEEGDKD"
"RKRARVCSYQSERSNLSGRGHVNNSREGDRFMNRKRTRNWDEAGNNKKKRECNNYRRDGRDR"
"EVRGYWERDKVGSNELVYRSGTWEADHERDVKKVSGGNRECDVKAEENKSKPEERKEKVVEE"
"QARRYQLDVLEQAKAKNTIAFLETGAGKTLIAILLIKSVHKDLMSQNRKMLSVFLVPKVPLV"
"YQVPPNKKHQAEVIRNQTCFQVGHYCGEMGQDFWDSRRWQREFESKQFLKLTSFFLFSSTQV"
"LVMTAQILLNILRHSIIRMETIDLLILDECHHAVKKHPYSLVMSEFYHTTPKDKRPAIFGMT"
"ASPVNLKGVSSQVDCAIKIRNLETKLDSTVCTIKDRKELEKHVPMPSEIVVEYDKAATMWSL"
"HETIKQMIAAVEEAAQASSRKSKWQFMGARDAGAKDELRQVYGVSERTESDGAANLIHKLRA"
"INYTLAELGQWCAYKVGQSFLSALQSDERVNFQVDVKFQESYLSEVVSLLQCELLEGAAAEK"
"VAAEVGKPENGNAHDEMEEGELPDDPVVSGGEHVDEVIGAAVADGKVTPKVQSLIKLLLKYQ"
"HTADFRAIVFVERVVAALVLPKVRIKVFAELPSLSFIRCASMIGHNNSQEMKSSQMQDTISK"
"FRDGHVTLLVATSVAEEGLDIRQCNVVMRFDLAKTVLAYIQSRGRARKPGSDYILMVERYIK"
"SFKNYILIFVTTGHQISTDMSTCVTCRGNVSHAAFLRNARNSEETLRKEAIERTDLSHLKDT"
"SRLISIDAVPGTVYKVEATGAMVSLNSAVGLVHFYCSQLPGDRYAILRPEFSMEKHEKPGGH"
"TEYSCRLQLPCNAPFEILEGPVCSSMRLAQQVDIIVSACKKLHEMGAFTDMLLPDKGSGQDA"
"EKADQDDEGEPVPGTARHREFYPEGVADVLKGEWVSSGKEVCESSKLFHLYMYNVRCVDFGS"
"SKDPFLSEVSEFAILFGNELDAEVLSMSMDLYVARAMITKASLAFKGSLDITENQLSSLKKF"
"HVRLMSIVLDVDVEPSTTPWDPAKAYLFVPVTDNTSMEPIKGINWELVEKITKTTAWDNPLQ"
"RARPDVYLGTNERTLGGDRREYGFGKLRHNIVFGQKSHPTYGIRGAVASFDVVRASGLLPVR"
"DAFEKEVEEDLSKGKLMMADGCMVAEDLIGKIVTAAHSGKRFYVDSICYDMSAETSFPRKEG"
"YLGPLEYNTYADYYKQKIYVVQDRLFFYFLHNLRLLRLYKSSSIMLFIRYGVDLNCKQQPLI"
"KGRGVSYCKNLLSPRFEQSGESETVLDKTYYVFLPPELCVVHPLSGSLIRGAQRLPSIMRRV"
"ESMLLAVQLKNLISYPIPTSKILEALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYPQ"
"KHEGQLTRMRQQMVSNMVLYQFALVKGLQSYIQADRFAPSRWSAPGVPPVFDEDTKDGGSSF"
"FDEEQKPVSEENSDVFEDGEMEDGELEGDLSSYRVLSSKTLADVVEALIGVYYVEGGKIAAN"
"HLMKWIGIHVEDDPDEVDGTLKNVNVPESVLKSIDFVGLERALKYEFKEKGLLVEAITHASR"
"PSSGVSCYQRLEFVGDAVLDHLITRHLFFTYTSLPPGRLTDLRAAAVNNENFARVAVKHKLH"
"LYLRHGSSALEKQVNKIKKQSILFSKSFKCLTVWLLFVFQIREFVKEVQTESSKPGFNSFGL"
"GDCKAPKVLGDIVESIAGAIFLDSGKDTTAAWKVFQPLLQPMVTPETLPMHPVRELQERCQQ"
"QAEGLEYKASRSGNTATVEVFIDGVQVGVAQNPQKKMAQKLAARNALAALKEKEIAESKEKH"
"INNGNAGEDQGENENGNKKNGHQPFTRQTLNDICLRKNWPMPSYRCVKEGGPAHAKRFTFGV"
'RVNTSDRGWTDECIGEPMPSVKKAKDSAAVLLLELLNKTFS"',
),
),
),
(
"CDS",
"complement(join("
"31084..31126,31223..31304,31341..31515,31635..31700,31790..31897,"
"31984..32049,32133..32161,32249..32372"
"))",
(
(
"/note=",
'"putative inorganic pyrophosphatase gi|3510259; similar to '
'ESTs gb|T42316, gb|AI994042.1, gb|AI994013.1, emb|Z29202"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.5"'),
("/protein_id=", '"AAF26475.1"'),
("/db_xref=", '"GI:6715648"'),
(
"/translation=",
'"MSEETKDNQRLQRPAPRLNERILSSLSRRSVAAHPWHDLEIGPGAPQIFNVVVEITKGSKV'
"KYELDKKTGLIKVDRILYSSVVYPHNYGFVPRTLCEDNDPIDVLVIMQEPVLPGCFLRARAI"
"GLMPMIDQGEKDDKIIAVCVDDPEYKHYTDIKELPPHRLSEIRRFFEDCILFLQCSSLFISI"
'DLSTNKKNENKEVAVNDFLPSESAVEAIQYSMDLYAEYILHTLRR"',
),
),
),
(
"CDS",
"complement(join("
"33694..34029,34103..35173,35269..35349,35432..35701,36326..36387,"
"36512..36623,36725..36763"
"))",
(
(
"/note=",
'"putative late elongated hypocotyl emb|CAA07004; similar to '
'ESTS gb|AI993521.1, gb|AA650979"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.6"'),
("/protein_id=", '"AAF26474.1"'),
("/db_xref=", '"GI:6715647"'),
(
"/translation=",
'"MDTNTSGEELLAKARKPYTITKQRERWTEDEHERFLEALRLYGRAWQRIEEHIGTKTAVQI'
"RSHAQKFFTKFGKAHSFWFTFQLEKEAEVKGIPVCQALDIEIPPPRPKRKPNTPYPRKPGNN"
"GTSSSQVSSAKDAKLVSSASSSQLNQAFLDLEKMPFSEKTSTGKENQDENCSGVSTVNKYPL"
"PTKVSGDIETSKTSTVDNAVQDVPKKNKDKDGNDGTTVHSMQNYPWHFHADIVNGNIAKCPQ"
"NHPSGMVSQDFMFHPMREETHGHANLQATTASATTTASHQAFPACHSQDDYRSFLQISSTFS"
"NLIMSTLLQNPAAHAAATFAASVWPYASVGNSGDSSTPMSSSPPSITAIAAATVAAATAWWA"
"SHGLLPVCAPAPITCVPFSTVAVPTPAMTEMDTVENTQPFEKQNTALQDQNLASKSPASSSD"
"DSDETGVTKLNADSKTNDDKIEEVVVTAAVHDSNTAQKKNLVDRSSCGSNTPSGSDAETDAL"
"DKMEKDKEDVKETDENQPDVIELNNRKIKMRDNNSNNNATTDSWKEVSEEGRIAFQALFARE"
"RLPQSFSPPQVAENVNRKQSDTSMPLAPNFKSQDSCAADQEGVVMIGVGTCKSLKTRQTGFK"
'PYKRCSMEVKESQVGNINNQSDEKVCKRLRLEGEAST"',
),
),
),
(
"CDS",
"complement(join("
"38600..38756,38838..38989,39111..39516,39915..40031,40377..40579"
"))",
(
(
"/note=",
'"similar to Medicago truncatula MtN2 gi|3193308; similar to '
'EST gb|H77065"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.7"'),
("/protein_id=", '"AAF26473.1"'),
("/db_xref=", '"GI:6715646"'),
(
"/translation=",
'"MAGDMQGVRVVEKYSPVIVMVMSNVAMGSVNALVKKALDVGVNHMVIGAYRMAISALILVP'
"FAYVLERASLMQFFFLLGLSYTSATVSCALVSMLPAITFALALIFRTENVKILKTKAGMLKV"
"IGTLICISGALFLTFYKGPQISNSHSHSHGGASHNNNDQDKANNWLLGCLYLTIGTVLLSLW"
"MLFQGTLSIKYPCKYSSTCLMSIFAAFQCALLSLYKSRDVNDWIIDDRFVITVIIYAGVVGQ"
"AMTTVATTWGIKKLGAVFASAFFPLTLISATLFDFLILHTPLYLGSVIGSLVTITGLYMFLW"
'GKNKETESSTALSSGMDNEAQYTTPNKDNDSKSPV"',
),
),
),
(
"CDS",
"complement(join("
"45150..45261,45343..45656,45719..45847,46075..46313,47448..47684,"
"47777..48554,48638..48868"
"))",
(
(
"/note=",
'"putative pyruvate dehydrogenase E1 alpha subunit gi|2454182; '
"similar to ESTs emb|Z48417, gb|AW039459.1, gb|T15146, "
'emb|Z48416, gb|AF066871, gb|T76832, gb|AI996061.1"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.8"'),
("/protein_id=", '"AAF26472.1"'),
("/db_xref=", '"GI:6715645"'),
(
"/translation=",
'"MATAFAPTKLTATVPLHGSHENRLLLPIRLAPPSSFLGSTRSLSLRRLNHSNATRRSPVVS'
"VQEVVKEKQSTNNTSLLITKEEGLELYEDMILGRSFEDMCAQMYYRGKMFGFVHLYNGQEAV"
"STGFIKLLTKSDSVVSTYRDHVHALSKGVSARAVMSELFGKVTGCCRGQGGSMHMFSKEHNM"
"LGGFAFIGEGIPVATGAAFSSKYRREVLKQDCDDVTVAFFGDGTCNNGQFFECLNMAALYKL"
"PIIFVVENNLWAIGMSHLRATSDPEIWKKGPAFGMPGVHVDGMDVLKVREVAKEAVTRARRG"
"EGPTLVECETYRFRGHSLADPDELRDAAEKAKYAARDPIAALKKYLIENKLAKEAELKSIEK"
"KIDELVEEAVEFADASPQPGRSQLLENVFADPKGFGIGPDGRYRSQPLQIKVSSSELSVLDE"
"EKEEEVVKGEAEPNKDSVVSKAEPVKKPRPCELYVCNIPRSYDIAQLLDMFQPFGTVISVEV"
"VSRNPQTGESRGSGYVTMGSINSAKIAIASLDGTVRARETKKQEVGGREMRVRYSVDMNPGT"
"RRNPEVLNSTPKKILMYESQHKVYVGNLPWFTQPDGLRNHFSKFGTIVSTRVLHDRKTGRNR"
'VFAFLSFTSGEERDAALSFNGTVNNMKVAESSSEKVSRRVSRKPTVLLLLQRHLLDTNNV"',
),
),
),
(
"CDS",
"complement(join(49986..50039,50121..50333,50585..50656))",
(
(
"/note=",
'"similar to acidic ribosomal protein p1 gi|2252857; '
'similar to ESTs gb|T42111, gb|AI099979, gb|AA728491"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.9"'),
("/protein_id=", '"AAF26471.1"'),
("/db_xref=", '"GI:6715644"'),
(
"/translation=",
'"MSTVGELACSYAVMILEDEGIAITADKIATLVKAAGVSIESYWPMLFAKMAEKRNVTDLIM'
'NVGAGGGGGAPVAAAAPAAGGGAAAAPAAEEKKKDEPAEESDGDLGFGLFD"',
),
),
),
(
"CDS",
"join("
"51941..52048,52136..52432,52640..52885,53186..53326,53405..54196"
")",
(
("/note=", '"hypothetical protein"'),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.10"'),
("/protein_id=", '"AAF26462.1"'),
("/db_xref=", '"GI:6715635"'),
(
"/translation=",
'"MGKKNGSSSWLTAVKRAFRSPTKKDHSNDVEEDEEKKREKRRWFRKPATQESPVKSSGISP'
"PAPQEDSLNVNSKPSPETAPSYATTTPPSNAGKPPSAVVPIATSASKTLAPRRIYYARENYA"
"AVVIQTSFRGYLARRALRALKGLVKLQALVRGHNVRKQAKMTLRCMQALVRVQSRVLDQRKR"
"LSHDGSRKSAFSDSHAVFESRYLQDLSDRQSMSREGSSAAEDWDDRPHTIDAVKVMLQRRRD"
"TALRHDKTNLSQAFSQKMWRTVGNQSTEGHHEVELEEERPKWLDRWMATRPWDKRASSRASV"
"DQRVSVKTVEIDTSQPYSRTGAGSPSRGQRPSSPSRTSHHYQSRNNFSATPSPAKSRPILIR"
"SASPRCQRDPREDRDRAAYSYTSNTPSLRSNYSFTARSGCSISTTMVNNASLLPNYMASTES"
"AKARIRSHSAPRQRPSTPERDRAGLVKKRLSYPVPPPAEYEDNNSLRSPSFKSVAGSHFGGM"
'LEQQSNYSSCCTESNGVEISPASTSDFRNWLR"',
),
),
),
(
"CDS",
"complement(57094..58680)",
(
(
"/note=",
'"putative fatty acid elongase 3-ketoacyl-coA synthase 1 '
"gi|4091810; similar to ESTs gb|T42377, gb|N96054, gb|T44368, "
'gb|AI999379.1, emb|Z26005"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.11"'),
("/protein_id=", '"AAF26470.1"'),
("/db_xref=", '"GI:6715643"'),
(
"/translation=",
'"MERTNSIEMDRERLTAEMAFRDSSSAVIRIRRRLPDLLTSVKLKYVKLGLHNSCNVTTILF'
"FLIILPLTGTVLVQLTGLTFDTFSELWSNQAVQLDTATRLTCLVFLSFVLTLYVANRSKPVY"
"LVDFSCYKPEDERKISVDSFLTMTEENGSFTDDTVQFQQRISNRAGLGDETYLPRGITSTPP"
"KLNMSEARAEAEAVMFGALDSLFEKTGIKPAEVGILIVNCSLFNPTPSLSAMIVNHYKMRED"
"IKSYNLGGMGCSAGLISIDLANNLLKANPNSYAVVVSTENITLNWYFGNDRSMLLCNCIFRM"
"GGAAILLSNRRQDRKKSKYSLVNVVRTHKGSDDKNYNCVYQKEDERGTIGVSLARELMSVAG"
"DALKTNITTLGPMVLPLSEQLMFLISLVKRKMFKLKVKPYIPDFKLAFEHFCIHAGGRAVLD"
"EVQKNLDLKDWHMEPSRMTLHRFGNTSSSSLWYEMAYTEAKGRVKAGDRLWQIAFGSGFKCN"
'SAVWKALRPVSTEEMTGNAWAGSIDQYPVKVVQ"',
),
),
),
(
"CDS",
"complement(join(59508..59665,61670..61826,63133..63513))",
(
("/note=", '"hypothetical protein"'),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.12"'),
("/protein_id=", '"AAF26469.1"'),
("/db_xref=", '"GI:6715642"'),
(
"/translation=",
'"MEKRSDSESVEILGDWDSPPPEERIVMVSVPTSPESDYARSNQPKEIESRVSDKETASASG'
"EVAARRVLPPWMDPSYEWGGGKWKVDGRKNKNKKEKEKEKEEIIPFKEIIEALLGNSGDKVQ"
"QDNKVFEVAPSLHVVELRKTGDDTLEFHKVYFRFNLYQPVQLPLILFVVIRFSMLKIIHYHQ"
'FTMAHIKEFVCMWDTHLYKEITNLNIWDTLSSTLVLAIWTVNASHE"',
),
),
),
(
"CDS",
"complement(join("
"64100..64177,64272..64358,64453..64509,64603..64719,64812..64919,"
"65033..65158,65265..65354,65435..65566,65809..65862,65964..66044,"
"66152..66259,66380..66451,66537..66599,67026..67214"
"))",
(
(
"/note=",
'"similar to wpk4 protein kinase dbj|BAA34675; similar to ESTs '
'dbj|AB015122, gb|AI997157.1"',
),
("/codon_start=", "1"),
("/evidence=", "not_experimental"),
("/product=", '"T25K16.13"'),
("/protein_id=", '"AAF26468.1"'),
("/db_xref=", '"GI:6715641"'),
(
"/translation=",
'"MSGSRRKATPASRTRVGNYEMGRTLGEGSFAKVKYAKNTVTGDQAAIKILDREKVFRHKMV'
"EQLKREISTMKLIKHPNVVEIIEVMASKTKIYIVLELVNGGELFDKIAQQGRLKEDEARRYF"
"QQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDFGLSAFSRQVREDGLLHTACGTPNY"
"VAPEVLSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYKRVRICKAEFSCPPWFSQ"
"GAKRVIKRILEPNPITRISIAELLEDEWFKKGYKPPSFDQDDEDITIDDVDAAFSNSKECLV"
"TEKKEKPVSMNAFELISSSSEFSLENLFEKQAQLVKKETRFTSQRSASEIMSKMEETAKPLG"
"FNVRKDNYKIKMKGDKSGRKGQLSVATEVFEVAPSLHVVELRKTGGDTLEFHKVCDSFYKNF"
'SSGLKDVVWNTDAAAEEQKQ"',