User: Erin_Ensembl
Erin_Ensembl • 220
- Reputation:
- 220
- Status:
- Trusted
- Location:
- EMBL-EBI
- Website:
- http://www.ensembl.info/
- Twitter:
- @mycoacia
- Last seen:
- 8 hours ago
- Joined:
- 1 year, 4 months ago
- Email:
- e*******@ebi.ac.uk
Posts by Erin_Ensembl
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Answer:
A: How to use dbSNP database?
... If you just have a handful of genes you can look them up in Ensembl, which hosts dbSNP data.
Go to [Ensembl][1] and search for your gene, e.g. STAR. Click on the results to go to the gene tab and find the [Variant table][2] in the left-hand navigation panel. You can use the filter options above th ...
written 13 days ago by
Erin_Ensembl • 220
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... You can search for your gene in [Expression atlas][1], where you can see its basal expression and it's expression in certain experimental conditions.
[1]: https://www.ebi.ac.uk/gxa/home ...
written 13 days ago by
Erin_Ensembl • 220
2
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Answer:
A: How to compare two proteomes
... Sounds to me like you just want to find (or rather exclude) orthologues of protein coding genes between a vertebrate species and drosophila.
You can do this across the whole genome in Ensembl's [BioMart][1] - video tutorial [here][2].
Step 1: Choose Ensembl Genes as your database, then choose a ...
written 13 days ago by
Erin_Ensembl • 220
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Comment:
C: ID and Variants in VCF
... Yes that looks correct to me! ...
written 15 days ago by
Erin_Ensembl • 220
0
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113
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Comment:
C: MAF format help
... I'm not sure... it may refer to a super contig (long stretch of sequence not yet assembled into chromosomes). Or a part of an alternate assembly (i.e. not part of the main chromosome level assembly, a haplotypic region). I don't know what 'DroPer1' is so I can't really comment further. ...
written 19 days ago by
Erin_Ensembl • 220
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Answer:
A: ID and Variants in VCF
... **To answer question 1:**
A better way to think of it is that each row in the VCF file is a specific variant location in the genome. For a SNP, there's only 4 possible outcomes for the nucleotide - A,C,T or G. One of these nucleotides is going to be the reference, so only 3 options in the alternate ...
written 20 days ago by
Erin_Ensembl • 220
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Comment:
C: MAF format help
... There's another post on this topic: https://www.biostars.org/p/190611/ ...
written 20 days ago by
Erin_Ensembl • 220
1
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2
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113
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Comment:
C: MAF format help
... No worries. Yes I think that it is correct. The MAF file stores information on alignment blocks, regions of the genomes that are similar. Whichever pipeline was used to create the multiple alignment will have searched across the genome for similar regions. There's no guarantee that the most similar ...
written 20 days ago by
Erin_Ensembl • 220
2
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2
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113
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Answer:
A: MAF format help
... You can find the MAF format description from UCSC [here][1]. This is a fairly standard file format and is also used by Ensembl.
There's a section there that says 'lines starting with s' which is your sequences within your alignment block. If you want to define your genomic coordinates you will ne ...
written 21 days ago by
Erin_Ensembl • 220
0
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2
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118
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Answer:
A: tools for finding paralogues
... If you know the gene name (i.e. the HGNC symbol), or a stable ID of the database you can use Ensembl to find the paralogues. Here is an example for the gene [MCM6][1]. If you want further help with browsing Ensembl for comparative genomics data you can watch our YouTube [comparative genomics videos] ...
written 4 weeks ago by
Erin_Ensembl • 220
Latest awards to Erin_Ensembl
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Fasta file and GTF file for STAR alignment
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5 months ago,
created an answer with at least 3 up-votes.
For A: Fasta file and GTF file for STAR alignment
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6 months ago,
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For A: Fasta file and GTF file for STAR alignment
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