User: The Last Word

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The Last Word160
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Posts by The Last Word

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Comment: C: Updating from old geneset to new with BLAST
... can you link me to the page of the transcriptome genomax? I can't seem to find it. Thx ...
written 6 weeks ago by The Last Word160
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Comment: C: Updating from old geneset to new with BLAST
... I was using the transcriptiome, so I guess, I will retrieve the full sequences for gene matches and use those. I was thinking that the genome might be a bit too big to really work with it. ...
written 7 weeks ago by The Last Word160
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Comment: C: Updating from old geneset to new with BLAST
... Just curious, I should be able to use these oligo sequences to BLAST and find homologous in other species can't I? For using these Apis genes to find homologous genes in Drosophila melanogaster. ...
written 7 weeks ago by The Last Word160
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Comment: C: Updating from old geneset to new with BLAST
... also the oligosequences I have are atleast 60 bases in length. I saw online that -short is used in the cases of sequences being less than 50 bases. ...
written 7 weeks ago by The Last Word160
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Comment: C: Updating from old geneset to new with BLAST
... I was thinking to use BLAST against the official geneset OGS3.2 listed here which is built on Amel 4.5. The next part was using the gene names to find their homologoues in the D. melanogaster gene database if possible. Where did you find the transcriptome? I guess BLAST against the transcriptome, ge ...
written 7 weeks ago by The Last Word160
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Updating from old geneset to new with BLAST
... I have set of genes and its sequences belonging to an old sequencing experiment. A new geneset has been released for the organism with new gene ids and its sequences. I have BLAST set up to run locally. I am aware that I need to BLAST gene sequences in the old geneset with the new ones so as to know ...
gene written 7 weeks ago by The Last Word160 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: Convert beebase ids
... Found it Genomax. Its https://www.ebi.ac.uk/arrayexpress/arrays/A-MEXP-755/?ref=E-TABM-953 . In that paper, in the methods section, he has mentioned some other studies done on the same array. Thank you for your help and guidance. ...
written 7 weeks ago by The Last Word160
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Comment: C: Convert beebase ids
... I am actually working on this network https://hood-price.systemsbiology.org/research/honeybee-transcriptional-regulatory-network/ . The paper linked to it is https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755009/ . I did reread the paper for this information but other than stating that the brain tran ...
written 7 weeks ago by The Last Word160
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Comment: C: Convert beebase ids
... I wanted to ask a question. Here is another oligonucleotide array https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16023 with sequences for the beebase IDs. The sequences in the set that you gave earlier and the ones in this are different. Any idea why that would be the case. I was actually usi ...
written 7 weeks ago by The Last Word160
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Comment: C: Convert beebase ids
... Hi genomax, I think I found the problem. These ids are from official gene set v1.0 for apis mellifera. The latest geneset is OGS3.2. Hymenopteramine is tuned to retrieve ids from only this new dataset. I found a paper that mapped these gene ids to the new geneset and they say they used BLAST but I c ...
written 7 weeks ago by The Last Word160

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