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Merge pull request #1258 from nextstrain/feat/aa-ancestral
feat: allow reconstruction of amino acid sequences
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export AUGUR="${AUGUR:-$TESTDIR/../../../../bin/augur}" |
26 changes: 26 additions & 0 deletions
26
tests/functional/ancestral/cram/default-nucleotide-reconstruction.t
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Setup | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Infer ancestral sequences for the given tree and alignment. | ||
The default is to infer ambiguous bases, so there should not be N bases in the inferred output sequences. | ||
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$ ${AUGUR} ancestral \ | ||
> --tree $TESTDIR/../data/tree.nwk \ | ||
> --alignment $TESTDIR/../data/aligned.fasta \ | ||
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \ | ||
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null | ||
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$ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" | ||
[1] | ||
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Check that the reference length was correctly exported as the nuc annotation | ||
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$ grep -A 6 'annotations' "$CRAMTMP/$TESTFILE/ancestral_mutations.json" | ||
"annotations": { | ||
"nuc": { | ||
"end": 10769, | ||
"start": 1, | ||
"strand": "+", | ||
"type": "source" | ||
} |
16 changes: 16 additions & 0 deletions
16
tests/functional/ancestral/cram/infer-ambiguous-nucleotides.t
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Setup | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Infer ancestral sequences for the given tree and alignment, explicitly requesting that ambiguous bases are inferred. | ||
There should not be N bases in the inferred output sequences. | ||
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$ ${AUGUR} ancestral \ | ||
> --tree $TESTDIR/../data/tree.nwk \ | ||
> --alignment $TESTDIR/../data/aligned.fasta \ | ||
> --infer-ambiguous \ | ||
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \ | ||
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null | ||
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$ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" | ||
[1] |
15 changes: 15 additions & 0 deletions
15
tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t
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Setup | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Try to infer ancestral amino acid sequences without all required arguments. | ||
This should fail. | ||
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$ ${AUGUR} ancestral \ | ||
> --tree $TESTDIR/../data/tree.nwk \ | ||
> --alignment $TESTDIR/../data/aligned.fasta \ | ||
> --annotation $TESTDIR/../data/zika_outgroup.gb \ | ||
> --genes ENV PRO \ | ||
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null | ||
ERROR: For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences. | ||
[2] |
26 changes: 26 additions & 0 deletions
26
tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
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Setup | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Infer ancestral nucleotide and amino acid sequences using a root sequence that | ||
was used for alignment. This additional argument allows the ancestral command to | ||
assign mutations on the branch leading to the inferred root (differences between | ||
the "root" used as an alignment reference and the inferred most recent common | ||
ancestor). | ||
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$ ${AUGUR} ancestral \ | ||
> --tree $TESTDIR/../data/tree.nwk \ | ||
> --alignment $TESTDIR/../data/aligned.fasta \ | ||
> --annotation $TESTDIR/../data/zika_outgroup.gb \ | ||
> --root-sequence $TESTDIR/../data/zika_outgroup.gb \ | ||
> --genes ENV PRO \ | ||
> --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \ | ||
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null | ||
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Check that the reference length was correctly exported as the nuc annotation | ||
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$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \ | ||
> --exclude-regex-paths "['seqid']" -- \ | ||
> "$TESTDIR/../data/ancestral_mutations_with_root_sequence.json" \ | ||
> "$CRAMTMP/$TESTFILE/ancestral_mutations.json" | ||
{} |
27 changes: 27 additions & 0 deletions
27
tests/functional/ancestral/cram/infer-amino-acid-sequences.t
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Setup | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Infer ancestral nucleotide and amino acid sequences. | ||
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$ ${AUGUR} ancestral \ | ||
> --tree $TESTDIR/../data/tree.nwk \ | ||
> --alignment $TESTDIR/../data/aligned.fasta \ | ||
> --annotation $TESTDIR/../data/zika_outgroup.gb \ | ||
> --genes ENV PRO \ | ||
> --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \ | ||
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \ | ||
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" \ | ||
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_%GENE.fasta" > /dev/null | ||
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Check that the reference length was correctly exported as the nuc annotation | ||
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$ grep -E "\"(ENV|PRO|nuc)\": {" "$CRAMTMP/$TESTFILE/ancestral_mutations.json" | ||
"ENV": { | ||
"PRO": { | ||
"nuc": { | ||
Check that internal nodes have ancestral amino acid sequences. | ||
$ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV.fasta" | wc -l | ||
\s*8 (re) |
16 changes: 16 additions & 0 deletions
16
tests/functional/ancestral/cram/keep-ambiguous-nucleotides.t
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Setup | ||
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$ source "$TESTDIR"/_setup.sh | ||
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Infer ancestral sequences for the given tree and alignment, explicitly requesting that ambiguous bases are NOT inferred. | ||
There should be N bases in the inferred output sequences. | ||
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$ ${AUGUR} ancestral \ | ||
> --tree $TESTDIR/../data/tree.nwk \ | ||
> --alignment $TESTDIR/../data/aligned.fasta \ | ||
> --keep-ambiguous \ | ||
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \ | ||
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" > /dev/null | ||
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$ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" | head -n 1 | ||
NNNNNNNNNNNNGACAGTTCGAGTTTGAAGCGAAAGCTAGCAACAGTATCAACAGGTTTT |
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>BRA/2016/FC_6706 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>COL/FLR_00008/2015 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>Colombia/2016/ZC204Se | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>DOM/2016/BB_0183 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>EcEs062_16 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>HND/2016/HU_ME59 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>PAN/CDC_259359_V1_V3/2015 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>PRVABC59 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>VEN/UF_1/2016 | ||
SPQDNQMAIIIMVAVGLLGLITA | ||
>ZKC2/2016 | ||
SPQDNQMAIIIMVAVGLLGLITA |
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>BRA/2016/FC_6706 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA | ||
MA | ||
>COL/FLR_00008/2015 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA | ||
MA | ||
>Colombia/2016/ZC204Se | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA | ||
MA | ||
>DOM/2016/BB_0183 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA | ||
MA | ||
>EcEs062_16 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA | ||
MA | ||
>HND/2016/HU_ME59 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA | ||
MA | ||
>PAN/CDC_259359_V1_V3/2015 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA | ||
MA | ||
>PRVABC59 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMETIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA | ||
MA | ||
>VEN/UF_1/2016 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKDAMEIIKKFKKDLAAMLRIINARKEKKRRGAETSVGIVGLLLTTA | ||
MA | ||
>ZKC2/2016 | ||
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK | ||
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTNVGIVGLLLTTA | ||
MA |
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>BRA/2016/FC_6706 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>COL/FLR_00008/2015 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>Colombia/2016/ZC204Se | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>DOM/2016/BB_0183 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>EcEs062_16 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>HND/2016/HU_ME59 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>PAN/CDC_259359_V1_V3/2015 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>PRVABC59 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>VEN/UF_1/2016 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA | ||
>ZKC2/2016 | ||
IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYC | ||
YEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFA | ||
CSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATL | ||
GGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE | ||
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRL | ||
KGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLIT | ||
ANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGARR | ||
MAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTK | ||
NGSISLMCLALGGVLIFLSTAVSA |
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