Blitvak Week 11
From LMU BioDB 2015
Journal Club Presentations and Initial Project Work
Work done on 11/10
- A possible MOD covering B. cenocepacia was found: Burkholderia Genome Database
- A test search was conducted for 'Burkholderia cenocepacia J2315
11/12
- The possible MOD was accessed and a test search was conducted:
- It was noticed that most "locus tags" were in the format BCAL####
- Some of the tags included an A at the end
- It was noticed that instead of BCAL, some genes were BCAM or BCAS
- Another test search was performed to observe the total number of genes with an ID that begins with "BCA":
- This searched yielded 7341 records (potentially, 7341 different genes)
- A similar search was conducted using the term "BCAL", which should cover all of genes with IDs that start with "BCAL"
- This search yielded 3603 records
- Another search was done using "BCAM"
- This search yielded 2859 records
- A search was done which covered the term "BCAS"
- This search yielded 779 records
- The last three searches were summed, yielding 7241 records (100 are unaccounted for)
- An advanced search was done in order to find the 100 records with an unknown starting pattern:
- It was found that the last 100 records started with pBCA (100 results, only)
- In this last search, it was noticed that most of the tags only had 3 numbers and that some ended with a lowercase a
- Reviewing the website, it was noticed that "%" is interpreted as wildcard by the database. A search was then done using the term "BCA%a" in order to see the number of records that ended with an "A"; it was noticed that some of these results included a lower-case r before the numbers (looking at the other columns in the search result, such as "Product name", it was realized that the tags that included the r corresponded to genes encoding for different types of tRNA (which correspond to the different amino acids)