User: jahanshanzida

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Posts by jahanshanzida

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Comment: A: Mapping of novel peptide
... Yes, this is a follow-up question.I have got two peptide by PGA bioconductor in R.These are : VFLLPLCKSS PPLLDQDQIV LLRGWFLSTW NLKCPTSNHS LEFNGTLLCP LVEAFSLWKP RPLSLQN chr1:87627704-87627922_+::::LINC01140|-|F3|1 I have then collected nucleotide sequence from USCS genome browser ...
written 5 weeks ago by jahanshanzida0 • updated 5 weeks ago by RamRS23k
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Mapping of novel peptide
... Dear All, I have got a couple of novel peptides by using PGA of R Bioconductor package. Now I want to map these novel peptides into genomic context. By using which bioinformatics tool I can map my novel peptides into New TIS, novel exon, a novel gene, novel splicing, UTR translation. Thank you. ...
genome written 5 weeks ago by jahanshanzida0
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Comment: C: Match peptides to protein sequences and tell the position in R
... Thank you so much for your answer. ...
written 6 weeks ago by jahanshanzida0
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Comment: C: Novel peptide identification
... Thank you so much for the reply and consideration of my problem. ...
written 7 weeks ago by jahanshanzida0
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Comment: C: Novel peptide identification
... Dear manuel.belmadani, Thank you so much for your elaborate explanation. You were right . My peptides are very short . Your suggestions are very helpful. I hope will get some fruitful outcome by following these. Thanks for your time. Shanzida ...
written 7 weeks ago by jahanshanzida0
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Comment: C: PRIDE Mass-Spec Published data analysis?
... Hello, I have peptide 30,000 peptide sequences from human brain sample. I want to compare these peptides with the PRIDE database peptide sequence to see whether my peptide sequence is novel or not. I am facing two problems. Firstly, I have to download the pride dataset in Linux server because my c ...
written 7 weeks ago by jahanshanzida0
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Comment: C: Novel peptide identification
... Thank you so much for your reply. The length of my peptide sequences is 30,000, and it is very difficult to do these at the same time. I also tried to do a search by splitting but that also increases the rate of mistakes. That's why I tried to download peptide dataset in the Linux server and then co ...
written 7 weeks ago by jahanshanzida0
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Novel peptide identification
... Hello, I have peptide 30,000 peptide sequences from human brain sample. I want to compare these peptides with the PRIDE database peptide sequence to see whether my peptide sequence is novel or not. I am facing two problems. Firstly, I have to download the pride dataset in Linux server because my c ...
R written 7 weeks ago by jahanshanzida0
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Comment: A: Match peptides to protein sequences and tell the position in R
... Hello, I have peptide 30,000 peptide sequences from human brain sample. I want to compare these peptides with the PRIDE database peptide sequence to see whether my peptide sequence is novel or not. I am facing two problems. Firstly, I have to download the pride dataset in Linux server because my c ...
written 7 weeks ago by jahanshanzida0

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