Strategy-5

Genome to ORF's

In this strategy, TC-CLB genome was converted into ORF's using Prodigal tool. It predicted 1,21,349 ORFs from TC-CLB genome and further these ORFs were filtered and resulted into 1640 ORFs. Additionally, 1640 ORFs were again sorted by their antigenicity and 100 ORF were filtered out for comparative analysis.

Filters used in the process:-

  • PSORTb: Subcellular Localization keyword

  • PSORTb: Subcellular Localization score

  • BLASTp against Human: Non-Homology

  • ProtParam: Stability

  • FungalRV: Adhesion factor

  • VaxiJen: Antigenicity

Following file contains python notebook used for filtering process along with their outputs, While filtering, 1640 ORfs were predicted to be PVC(Potential vaccine candidates) and further analysed.

VaxiJen File: (Only 2000 proteins are processed in a single run. However, there are more than 56+ files, which can be accessed from the link):

https://drive.google.com/drive/folders/1VtifgYfmWEk4RSMtbPNPWAX_IvhZrSPc?usp=sharing


Top 100 proteins retrieved by Strategy-5


Top-100_Strategy-5.xlsx

Top 7 unique proteins:-

  1. XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  2. XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]

  3. RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]

  4. XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]

  5. AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]

  6. XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]

  7. XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]


Strategy-5 vs Strategy-1

No intersection of proteins were found upon filtering of proteins via Strategy-5 and Strategy-1.

Union of proteins in Strategy-5 and Strategy-1:-

Strategy-5:-

  1. XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  2. XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]

  3. RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]

  4. XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]

  5. AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]

  6. XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]

  7. XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]

Strategy-1:-

  1. XP_809166.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]

  2. XP_816522.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]

  3. XP_815016.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]

  4. XP_818708.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_821916.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  6. XP_804513.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  7. XP_816111.1 subtilisin-like serine peptidase [Trypanosoma cruzi strain CL Brener]

  8. XP_806816.1 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]

Strategy-5 vs Strategy-2

No intersection of proteins were found upon filtering of proteins via Strategy-5 and Strategy-2.

Union of proteins in Strategy-5 and Strategy-2:-

Strategy-5:-

  1. XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  2. XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]

  3. RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]

  4. XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]

  5. AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]

  6. XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]

  7. XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]

Strategy-2:-

  1. XP_809166.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]

  2. XP_811700.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]

  3. XP_822020.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]

  4. XP_804447.1 ubiquitin-conjugating enzyme E2 [Trypanosoma cruzi strain CL Brener]

  5. XP_807999.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  6. XP_806523.1 IgE-dependent histamine-releasing factor [Trypanosoma cruzi strain CL Brener]

  7. XP_808372.1 small nuclear ribonucleoprotein Sm-E [Trypanosoma cruzi strain CL Brener]

  8. XP_818708.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

Strategy-5 vs Strategy-3

No intersection of proteins were found upon filtering of proteins via Strategy-5 and Strategy-3.

Union of proteins in Strategy-5 and Strategy-3:-

Strategy-5:-

  1. XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  2. XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]

  3. RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]

  4. XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]

  5. AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]

  6. XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]

  7. XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]

Strategy-3:-

  1. XP_805056.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]

  2. XP_802955.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]

  3. XP_815016.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]

  4. XP_807308.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_821176.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  6. XP_804140.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  7. XP_816111.1 subtilisin-like serine peptidase [Trypanosoma cruzi strain CL Brener]

  8. XP_806816.1 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]

Strategy-5 vs Strategy-4

No intersection of proteins were found upon filtering of proteins via Strategy-5 and Strategy-4:-

Union of proteins in Strategy-5 and Strategy-4:-

Strategy-5:-

  1. XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  2. XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]

  3. RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]

  4. XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]

  5. AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]

  6. XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]

  7. XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]

Strategy-4:-

  1. XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]

  2. XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  3. XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  4. XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]

  6. XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]

  7. XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]

  8. XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi strain CL Brener]