Sarcina de lucru 23.02.

2019

1. Este dată secvența de nucleotide

ACAGCATTGTAACAGAGAAAGAAAGGAACATTTGAGCAAAAATGGTTCAAGCACAGCCTCTACAACATGT
TGGTAATGGTGCAGGGAAAGAAGATCTAGCTTATAATTTTGATCCAAGTGCTCCACCACCCTTCAAGATT
GCAGATATCAGAGCAGCAATTCCAAAGCATTGCTGGGAGAAGAACACATTGAGATCTCTGAGTTACGTTC
TGAGGGATGTGTTGATAGTTTCTGCATTGGTAGCTGCAGCAATTGGCTTCAATAGCTGGCTCTTCTGGCC
ACCCTATTGGTCTGCACAAGGCACAATGTTTTGGGCACTTTTTGTTCTTGGACATGATTGTGGTCATGGA
AGTTTTTCCAACAGTCCTATGTTGAACAGCATTGTGGGCCACATCTTGCACTCTTCAATCCTTGTACCAT
ACCATGGATGGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATG
GGTTCCGCTTTCAGAGAAAGTTTACAAGAATCTAGACAACATGACAAGAATGATGAGATTCACTCTTCCT
TTCCCCATCTTTGCATACCCCTTTTATTTGTGGAGCAGAAGCCCAGGAAAAGAAGGTTCTCATTTCAACC
CTTACAGCAACTTGTTCTCCCCTGGTGAGAGAAGAGATGTGATAACTTCAACTCTTTGTTGGGGCATCAT
GCTTTCTCTGCTTCTCTATCTTTCCCTCACATTGGATCCACTTTTTATGTTCAAGCTTTATGGGGTTCCT
TATTTGATCTTCGTCGTGTGGCTGGATTTCGTCACATACTTGCATCATCATGGTTACAAGCAGAAACTAC
CTTGGTACCGTGGCCAGGAATGGACTTATCTAAGGGGTGGTCTTACAACCGTAGATCGTGACTATGGTTG
GATCAACAACATTCACCATGACATTGGCACCCATGTCATCCATCACCTTTTCCCTCAGATTCCACATTAT
CATTTGGTTGAAGCGACTAAAGCAGCTAAGGCAGTGCTAGGAAAGTATTATCGTGAGCCTCAGAAATCAG
GGCCATTGCCACTTCATCTTATCAAGTACTTGCTACACAGCATAAGTCAGGATCACTTCGTTAGTGACTA
TGGTGACATTGTGTACTACCAAACTGATTCTCAGTTCCACAAAGATTCTTGGACCAAGTCCAACTAAAGT
TTTGATGCTACTACATTGACCTATTTTCTCATATGTTACCTAATCAAATCAATTAGGTGACATGTATAAG
CTTTCATAAATTATGCTAGAAATGTACTTACTGTTCAAAGCATGCTATGCTAGAAAAGAATCTATTTTTC
AATACCCAGA

Stabiliți identitatea acestei secvențe. Inserați info GenBank despre această secvență.
|n NCBI BLASTn se insereaza secventa propusa

Din Gen bank>

Glycine max omega-3 fatty acid desaturase D (FAD3-2b), mRNA
NCBI Reference Sequence: NM_001249746.2 Commented [P1]: Aici se poate insera PrtSc, dar este corect si
varianta pe care ati dat-o

2. Arătați reverse complement-ul acestei secvențe. descrieți cea mai simplă cale de a-l obține.

Se deschide secven’a, apoi din meniu Customize view se bifeaza Show reverse
complement se indica formatul FASTA
3. Identificați locația regiunii codificatoare (poziția nucleotidele de la 42 până la 1187).
Inserați PrtScn raportului de identificare.
Ne intoarcem la secventa primara [n GenBank ;i selectam
CDS 42..1187
 4. Efectuați analiza BLAST a regiunii codificatoare identificate in punctul precedent.
Selectați din lista de raport datele referitoare la alinierea secvenței CDS cu porțiunea
respectivă la Phaseolus vulgaris. Inserați PrtScn domeniului respectiv al raportului
tabelar.
Decshidem pagina noua NCDI BLAST si efectuam analiza BLAST pentru secventa respeciva Commented [P2]: Regiunea codificatoare

Glycine max omega-3 fatty acid desaturase D (FAD3-2b), mRNA Commented [P3]: Din raportul Blast, partea a treia select[m
alinierea secven’ei de interes cu secventa care apartine specie
Phaseolus vulgaris.
5. Prezentați în format FASTA porțiunea respectivă pentru Phaseolus vulgaris și secvența
Dupa asta inserati PrtSc respectiv
integrală din GenBank care conține această porțiune.

Commented [P4]: Acest PrtSc nu este necesar.

Commented [P5]: Aici trebuie sa notati ca este FASTA pentru

regiunea codificatoare.

Afara de aceasta trebuie sa inserati si FASTA pentru secventa

integral. Pentru aceasta debifati Select region si bifati Whole
sequence, apoi Upload si inserati PrtSc respectiv

6. Selectați suplimentar secvențe omoloage pentru Vigna radiata, Vigna angularis, Cajanus
cajan, Abrus precatorius, Lupinus angustifolius și generați un fișier Fasta în file cu extensiunea
txt.

>XM_007146711.1:134-1276 Phaseolus vulgaris hypothetical protein (PHAVU_006G068600g) mRNA, complete cds

ATGGTTCAAGCAGAAAATCTGCAACATTTTGGTAATGGGGGAAGGGAAGAAGATCAAACTTATTTTGATC
CAAGTGCTCCACCACCCTTTAAAATTGCAGATATCAGAGCAGCAATTCCCAAGCATTGCTGGGAGAAGAG

CATACTGAGATCTCTGAGTTATGTTCTCAGGGATGTCTTGGTGGTCACAGCATTAGTGGCTGCAGCAATT

GGCTTCAATAGCTGGTTCTTCTGGCCAGTCTATTGGCCTCTACAGGGAACAATGTTTTGGGCCCTGTTTG

TTCTTGGACATGATTGTGGGCATGGAAGTTTTTCAAACAATTCCAAGTTGAATAGCTTTGTGGGCCACAT

ATTGCACTCCTCAATCCTTGTACCATACAATGGGTGGAGAATCAGCCACAGGACTCACCACCAAAACCAT

GGACATGTTGAGAAGGATGAATCCTGGGTTCCGTTAACGGAGAAGGTTTACAAGAATCTAGACAACATGA

CAAGAATGCTGAGATACACTTTTCCTTTTCCAATCTTTGCATATCCCTTTTATCTGTGGAACAGAAGCCC

AGGGAAAGAAGGTTCCCATTTCAACCCTTACAGCAACTTGTTCTCTCCTGGTGAGAGAAAAGATGTGGTA

ACTTCAACCCTGTGTTGGGGCATCGTGCTTTCTGTGCTTCTCTATCTTTCCCTAACAATAGGTCCAATTT

TTATGCTCAAGCTCTATGGGGTACCCTATTTGATCTTCGTCGTGTGGCTGGATTTTGTCACCTATTTGCA

CCATCATGGTTACAGCCACAAACTACCTTGGTACCGTGGCCAGGAATGGAGTTATCTAAGGGGTGGTCTT

ACAACAGTAGATCGTGACTATGGTTGGATTAACAACGTTCACCATGACATTGGCACCCATGTTATCCATC

ACCTTTTCCCTCAAATTCCACATTACCATTTGGTGGAAGCGACTAAAGCAGCAAAATCAGTGCTTGGAAA

GTATTATCGTGAGCCTCAGAAATCTGGGCCATTGCCATTTCATCTATTGAAGTACTTGCTACACAGCATA

AGTCAGGATCACTTCGTTAGCGACTCTGGGGACATTGTGTACTATCAGACTGATTTCAAGCTCCACAAAG

ATTCTTGGACCAAGTCCAACTAA

Vigna radiata,

>NM_001317155.1:9-1151 Vigna radiata omega-3 fatty acid desaturase, endoplasmic reticulum (LOC106775023),
mRNA

ATGATTCAAGCACAAACTCTGCAACATTTTGGTAATGGGGCAAGGGAAGGAGATCAAAGTTATTTTGATC

CAGGTGCTCCACCACCCTTTAAGATTGCAGATATCAGAGCAGCAATTCCCAAGCATTGCTGGGAGAAAAG

CACACTCAGATCTCTGAGTTATGTTCTCAGGGATGTTTTAGTCGTCACAGCATTGGCGGCTTCAGCAATT

TCCTTCAATAGCTGGTTCTTCTGGCCACTCTATTGGCCTGCACAAGGCACAATGTTTTGGGCTCTGTTTG

TTCTTGGACATGATTGCGGGCATGGAAGTTTTTCAAACAGTTCCAAGTTGAATAGCTTTGTGGGCCACAT

CTTGCACTCCTTGATCCTTGTACCATACAATGGATGGAGAATCAGCCACAGGACTCACCACCAAAACCAC

GGCCATGTTGAGAAGGATGAATCCTGGGTTCCGTTAACGGAGAAGGTTTACAAGAATCTAGACGACATGA

CAAGAATGCTGAGATACTCTTTTCCTTTTCCAATCTTTGCATATCCCTTTTATTTGTGGAACAGAAGCCC

AGGGAAAGAAGGTTCTCATTTCAACCCTTACAGCAACTTGTTCTCCCCTGGTGAGAGAAAAGGCGTGGTA

ACTTCGACCCTGTGTTGGGGCATCGTTCTTTCTGTGCTTCTCTATCTTTCCCTAACAATAGGTCCAATTT

TCATGCTCAAGCTCTATGGGGTACCCTATTTGATCTTCGTCATGTGGCTCGATTTCGTCACCTACTTGCA

TCATCATGGTTACACGCATAAACTACCTTGGTACCGTGGCCAGGAATGGAGCTATCTAAGGGGTGGTCTT
ACAACAGTAGATCGTGACTATGGTTGGATTAACAACGTTCACCATGACATTGGCACCCATGTTATCCATC

ACCTTTTCCCTCAAATTCCACATTACCATTTGGTGGAAGCGACTAAATCAGCAAAATCAGTGCTTGGAAA

GTATTATCGTGAGCCTCAGAAATCTGGGCCATTGCCATTTCATCTATTGAAGTACTTGCTACAAAGCATA

AGTCAGGATCACTTCGTTAGCGACACTGGCGACATTGTGTACTATCAGACTGATCCCAAGCTCCACCAAG

ATTCTTGGACCAAGTCCAAGTAA

Vigna angularis,

>AP015038.1:15512512-15512807 Vigna angularis var. angularis DNA, chromosome 5, almost complete sequence,
cultivar: Shumari

ATGGTTCAAGCTCAAACTCTGCAGCATTTTGGTAATGGGGCAAGGGAAGGAGATCAAACTTATTTTGATC

CAGGTGCTCCACCACCCTTTAAGATTGCAGATATCAGAGCAGCAATTCCCAAGCATTGCTGGGAGAAAAG

CACACTGAGATCTCTCAGTTATGTTCTCAGGGATGTCTCAATGGTCACAGCATTGGCGGCTGCAGCAATT

GCCTTCAATAGCTGGTTCTTCTGGCCACTCTATTGGCCTGCACAAGGCACAATGTTTTGGGCCCTGTTTG

TTCTTGGACATGATTG Commented [P6]: Aici este doar una din cele 4 alinieri.
Trebuiau puse toate

Cajanus cajan,

>XM_020381423.1:89-1231 PREDICTED: Cajanus cajan omega-3 fatty acid desaturase, endoplasmic reticulum
(LOC109816410), mRNA

ATGGTTCAGGTTCTGTCTCTGCAACATGTTGGTAATGGGGCAGTTCTAGAGGATCAAACATGTTTTGATC

CAAGTGCTCCACCACCCTTTAAGATTGCAGATATCAGAGCAGCAATTCCCAAGCATTGTTGGGAGAAGAA

TCCATGGAGGTCTGTGAGTTATGTTGTGAGGGATGTGTTCATAGTCTTTGCATTGCTCTATGCTGCAATT

CGATTCAATACCTGGCTCTTCTGGCCTCTCTATTGGCCTGCTCAAGGCACCATGTTTTGGGCCCTTTTTG

TCCTTGGACATGATTGTGGCCATGGAAGTTTTTCAAACAGTCTCAAGTTGAATAGCCTGGTGGGCCACAT

CTTGCATTCCTCAATTCTTGTACCATACCATGGATGGAGGATTAGCCATAGGACTCACCACCAAAACCAT

GGACATGTGGAGAATGATGAATCATGGGTTCCGCTGACAGAGAAGGTTTACAAGAGCCTAGACAACATGA

CAAGAATGCTGAGATTCACTGTTCCTTTCCCCGTCTTTGCATACCCTTTTTATTTGTGGGGTAGAAGCCC

TGGAAAAGAAGGTTCTCACTTCAGCCCCTACAGCAACTTGTTCTCCCCTGGTGAGAGAAAAGATGTGGCG

ACTTCAACTCTGTGTTGGAGCATCATGCTATGTGTTCTTGTCTATCTATCAATCGTAATGGGTCCAATTT

TTATGTTCAAGCTCTATGGGGTACCCTATTTGATCTTCGTCATGTGGCTGGACTTCGTCACGTACTTGCA

TCATCATGGTTACAGTCAGAAACTACCGTGGTACCGTGGCAAGGAATGGAGTTATCTAAGAGGTGGTCTT

ACAACCATAGATCGTGATTACGGTTGGATCAACAACATTCACCATGACATTGGCACCCATGTCATTCATC

ACCTTTTCCCTCAAATTCCGCATTATCATTTGGTAGAAGCGACTAATTCAGCAAAAGCAGTGCTTGGAAA
GTATTATCGTGAGCCTCAGAAATCTGGGCCAGTGCCAGTCCATTTGGTGAAGTACTTGCTTCACAGCATA

AGTCAGGATCACTTCGTTAGCGACTCTGGAGACATTGTGTACTACCAGACTGATCCTGAGCTCCGCAAAG

ATTCTTGGACCAAATCCAACTAA

Abrus precatorius,

>XM_027478804.1:12-1149 PREDICTED: Abrus precatorius omega-3 fatty acid desaturase, endoplasmic

reticulum-like (LOC113849137), mRNA

AGCACAACATCTACAATATGTTAGCAATGGAGAAGGGCAAGGACAGCATCAAACTTATTTTGATCCAAGT

GCTCCTCCACCCTTTAAGATTGCCGAAATTAGAGCAGCAATTCCCAACCATTGTTGGGTCAAGAATCCAT

GGAGGTCTCTGAGTTATGTTCTAAGGGATGTTTTAGTAGTCACTGCATTGCTAGCTGCAGCAATTGGCTT

CAATAACTGGTTCTTCTGGCCTCTCTATTGGGTTGCTCAAGGAACAATGTTTTGGGCTTTATTTGTTCTT

GGACATGATTGTGGGCATGGAAGTTTTTCAAACAGTCCCAGGTTGAATAGCGTAGTGGGCCACATCTTGC

ACTCATCAATTCTTGTACCATACCATGGATGGAGAATTAGCCATAGAACTCACCATCAAAACCATGGACA

TGTTGAGAAGGATGAATCATGGGTTCCGCTGACAGAGAAGGTTTACAAGAGTCTAGACAACATGACAAGA

ACCATGAGATTCACTTTTCCTTTCCCCATCTTTGCATATCCCTTTTATTTGTGGAGCAGAAGCCCCGGAA

AGGAAGGCTCTCACTTCAACCCCTATAGCAACTTGTTTTCCCCTAGTGAAAGAAAAGATGTGCTAACTTC

AACACTCTGTTGGGTCATCATGCTTTCTGTGCTTCTCTCCCTGTCCTTCATAATGGGACCATTTTTTATG

TTTAAGCTCTATGGAGTTCCCTATTTGATCTTCATCATGTGGCTAGACTTGGTCACATACTTGCATCATC

ATGGTTACAAGCAGAAACTACCTTGGTACCGTGGCAAGGAATGGACTTATCTAAGGGGTGGTCTTACAAC

TGTGGATCGTGACTATGGTTGGATTAACAACATTCACCATGACATTGGCACTCATGTTATCCATCATCTT

TTTCCTCAAATCCCACATTATCATTTGCTTGAAGCGACGAAAGCTGCAAAACCAGTGCTAGGAAAGTATT

ATCGTGAGCCAGAGAAATCAGGGGCAGTGCCACTCCATCTAATAAAGTACTTGCTACACAGCATAAGTCA

GGACCACTTTGTGAGTAACTATGGTGACATTGTGTACTACCAAACTGATCCTCGCCTGCAGAGAAATTCT

TGGACCACGTCTAAGTAA

Lupinus angustifolius

>XM_019591465.1:137-1200 PREDICTED: Lupinus angustifolius omega-3 fatty acid desaturase, endoplasmic

reticulum-like (LOC109350266), mRNA

TTTTGATCCAAGTGCTCCACCACCCTTTAAGATAGCAGAAATTAGAGCTTCCATTCCTAAACATTGCTGG

GTGAAGAATCCATGGAAGTCTCTGAGTTATGTTCTTAGAGATGTTATTGTAGTCACTGCATTGATTGGTG

CAGCAATTTGGTTCAATAGTTGGTTCTTTTGGCCACTTTATTGGGTTGCTCAGGGTACAATGTTCTGGGC
TCTTTTTGTTCTTGGACATGATTGTGGCCATGGAAGCTTTTCAAACAGTTCCACGCTGAATAGCATTGTG

GGCCATATCTTGCACTCATCAATTCTTGTACCATACCATGGATGGAGAATTAGCCATAAAACTCACCATC

AACACCATGGACATGTTGAGAAGGATGAATCATGGGTTCCACTGCCAGAAAAGATTTACAAGAATCTAGA

CAACACGACTAAACTCTTGAGATTCACTCTGCCTTTCCCAATCTTTGCATATCCTTTTTACTTGTGGTAC

AGAAGCCCAGGAAAAGAGGGCTCTCATTTCAATCCATACAGCAACTTGTTCTCTCCCTCCGAGAGAAAAG

ATGTGATAACTTCAACCCTATGTTGGTCCATCATGTTTTCTGTGCTTCTCTATTTATCCATTACATTGGG

TCCATTTTTAATGTTTAAGGTCTATGGAGTACCCTATCTGGTCTTCGTCATGTGGCTGGACTTTGTCACA

TATTTGCACCACCATGGTTACAAGCAGAAACTACCTTGGTACCGCGGCCAGGAGTGGGACTATCTAAGGG

GTGGTCTTACAACCGTGGACCGTGACTATGGTTGGGTTAACAGCATTCACCATGACATTGGCACCCATGT

TATCCATCACCTTTTTCCTCAAATTCCTCATTACCATTTAATTGAAGCGACTGAAGCAGCAAAACCAGTG

CTTGGAAAATATTATCGTGAGCCTGAAAAATCTGGTCCAATCCCTTTCCATCTAATCACGTACTTGCTAC

ATAGTATAAAGCAAGATCACTTCGTGAGTGACACTGGAGACATTGTTTACTACCAAAATGATCCTAAGCT

TCAGAAATATTCTT

Si efectu[m redactare secventelor selectate pentru a fi introduse in programul de aliniere MUSCLE

 7. Realizați alinierea secvențelor selectate utilizând resursele Muscle – multiple Sequence
Alignment ( de ex.: http://www.ebi.ac.uk/Tools/msa/muscle/). Memorizați rezultatul sub
sub formă de file cu extincția .txt. Inserați fișierul obținut

Dup[ ce s/au efectuat redactarile in documentul TEXT, eliminind spatiile lasind in fata
secventelor selectate doar > ;I din rind nou secventele nucleotidice, deschidem programul
Muscle – multiple Sequence Alignment, introducem secventele selectate in prima
fereastra, se selcteaya formatul necesar in al 2 pas (Person Fasta) si obtinem

Apoi rezultatul obtinut se copie in document TEXT , se inchide si se descide acest document prin
Mesquit
8. Vizualizați alinierea cu ajutorul programului Mesquite. Editați alinierea prin eliminarea
sectoarelor de gaps-uri finale și inițiale dacă este cazul. Exportați fișierul în format
NEXUS.
Redactarea si eliminarea gapsurilor se efectueaza prin EDIT
Documentul deja redactat *shift edit cut pentru eliminarea gapsurilor si apoi se exporta in
NEXUS File, export, simple file nexus, ok, export , se da nume ;i se pastreaza in forma de
document TEXT
Apot documentul obtinut se deschide de pe masa de lucru prin formatul NotePad

9. Descrieți structura fișierului NEXUS și comparați-l cu fișierul FASTA.

Fisierul NEXUS include # , Dimensiunea, date despre ce este (DNA, etc), denumirea Commented [P7]: Tipul de format – NEXUS, Begin data, Date
despre numarul de taxoni si caractere, dupa care urmeaza matrice –
matricelui si denumirea date despre num[rul de taxoni si de caractere analizate adica secventele

Fasta Denumirea secventei si din rind nou ins[si secventa Commented [P8]: Semnul de inceput,

10. Identificati secventa

MTSTTSKVTFGKSIGFRKELNRRVNAYLEAENISPRDNPAMYLKTAIILAWVVSAWTFVVFGPDVLWMKLLGCTVLGFGVSAVGFNISHDGNH
GGYSKYQWVNYLSGLTHDAIGVSSYLWKFRHNVLHHTYTNILGHDVEIHGDELVRMSPSMEYRWYHRYQHWFIWFVYPFIPYYWSIADVQTML
FKRQYHDHEIPSPTWVDIATLLAFKAFGVAVFLIIPIAVGYSPLEAVIGASIVYMTHGLVACVVFMLAHVIEPAEFLDPDNLHIDDEWAIAQV
KTTVDFAPNNPIINWYVGGLNYQTVHHLFPHICHIHYPKIAPILAEVCEEFGVNYAVHQTFFGALAANYSWLKKMSINPETKAIEQLTV

Stabiliți, ce unitate proteică este prezentată. Completați un raport cu descrierea succesiunii

pașilor în stabilirea acestei unități cu utilizarea PrtScn-urilor semnificative.
 11. Identificați secvența nucleotidică translată în baza acestei secvențe proteice utilizand
tblastn. Completați un raport cu descrierea succesiunii pașilor în stabilirea acestei unități
cu utilizarea PrtScn-urilor semnificative.

Identical proteins
CDS 1..368

Meniu BLAST din NCBI

12.