Difference between revisions of "Blitvak Week 11"
From LMU BioDB 2015
(added note about updated database) |
(added unfamiliar and slightly unfamiliar biology terms (definitions to follow, soon)) |
||
| Line 1: | Line 1: | ||
| + | |||
==Journal Club Presentations and Initial Project Work== | ==Journal Club Presentations and Initial Project Work== | ||
===Work done on 11/10=== | ===Work done on 11/10=== | ||
| Line 25: | Line 26: | ||
*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) | *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) | ||
*In the latest news section of the database it was stated that there is an updated beta version of the MOD available (http://beta.burkholderia.com/); this updated website will be used in future work | *In the latest news section of the database it was stated that there is an updated beta version of the MOD available (http://beta.burkholderia.com/); this updated website will be used in future work | ||
| + | ===Preparation for Genome Paper Presentation=== | ||
| + | ====Unfamiliar Biology Terms from the Manuscript==== | ||
| + | *Saprophyte: | ||
| + | *Orthologous: | ||
| + | *Homologous: | ||
| + | *CDSs: | ||
| + | *Replicons: | ||
| + | *Concatenated (in relation to genomes): | ||
| + | *Genomic Island: | ||
| + | *Mobile genetic elements: | ||
| + | *Rearrangement: | ||
| + | *Prophage: | ||
| + | *In silico: | ||
| + | *Nonmucoid: | ||
| + | *Efflux system: | ||
| + | *Peritrichous: | ||
| + | *Fimbrial: | ||
Revision as of 05:15, 14 November 2015
Contents
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)
- In the latest news section of the database it was stated that there is an updated beta version of the MOD available (http://beta.burkholderia.com/); this updated website will be used in future work
Preparation for Genome Paper Presentation
Unfamiliar Biology Terms from the Manuscript
- Saprophyte:
- Orthologous:
- Homologous:
- CDSs:
- Replicons:
- Concatenated (in relation to genomes):
- Genomic Island:
- Mobile genetic elements:
- Rearrangement:
- Prophage:
- In silico:
- Nonmucoid:
- Efflux system:
- Peritrichous:
- Fimbrial:
