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Analyzing cDNA Sequences: Quality Check and Functional Predictions

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Dive into the intricate process of analyzing cDNA sequences! This guide walks you through the essential initial questions such as assessing the quality of your sequence, identifying a poly(A) tail, and locating the start of the cDNA insert. Learn how to use BLAST to compare your sequence against others, navigate reading frames, and determine the most likely protein coding functions based on BLAST results. This comprehensive analysis is crucial for researchers looking to understand the implications of their cDNA findings and enhance their molecular biology skills.

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Analyzing cDNA Sequences: Quality Check and Functional Predictions

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  1. Practice Clone 3 Download and get ready!

  2. After opening the sequence…. What questions do you start with? Is the sequence of good quality? Do you see a poly AAA tail? What does that mean? Where is the start of the cDNA insert?

  3. a. b c d e

  4. a. b c d e

  5. c d e b

  6. What country was this sequence published? A. Russia B. China C. US D. Japan E. France

  7. Blast N: nr/nt Blast N: estremember from other cDNA clones!

  8. BLAST X

  9. BLAST X Note the alignment! Where does our query start to match? What reading frame is the BLAST X in? A. 0 B. +1 C. +2 D. +3 E. at the Met

  10. Looking at the accession number record:

  11. a. b. c d. 1 mmfeyvlflsvylfsigiyglitsrnmvralmclelilnsvninlvtfsdifdsrqlkgd 61 ifsifviaiaaaeaaiglaivssiyrnrkstrinqsnlln n

  12. a. b. c.

  13. Blast P with the ENTIRE ORF

  14. Using the information in the Blast P, what does your protein most likely code for? Cytochrome C NADH dehydrogenase Acetylcholinesterase A transcription factor Both B and C

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