Originally posted by upendra_35
View Post
-
I've tried changing format but it doesn't work. I guess we should use TAIR10_pep... for BLAST DBs which is protein files. -
Sorry my bad.....i have used pep file and not cDNA file.Originally posted by hugh_hang View PostComment
-
Blast2GO is very particular about the format of the sequence ID used in FASTA files when you are creating custom BLAST databases. See this webpage for details about formatting your own BLAST DB for use with Blast2GO.Originally posted by hugh_hang View Post
A second thing to consider is do the IDs in you custom BLAST DB ('myid' in the example on the webpage) match IDs in the Blast2GO database. If the IDs don't match, Blast2GO won't be able to map them. Even if you reformatted the TAIR FASTA like the example in the tutorial and put the AT number in the proper position I'm not sure that TAIR AT numbers are in the Blast2GO database.
A workaround is to use this file from the TAIR site: At_GB_refseq_prot.gz. It is the same protein set but uses the NCBI RefSeq IDs and GI numbers for the IDs. For example:
Format this file according to the tutorial. You are sacrificing the AT numbers but it's pretty much a guarantee that the NCBI GIs are in the Blast2GO database.Code:>gi|240256448|ref|NP_200529.4| PSD2 (phosphatidylserine decarboxylase 2); phosphatidylserine decarboxylase [Arabidopsis thaliana]
Comment
-
Thank you very much kmcarr, very useful tips. Can't wait to start my Blast2Go annotation now. Thanks again.Originally posted by kmcarr View PostComment
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
Comment