mapping peptide sequences

Hi eveyone

I am wondering does anyone know how to map short peptide sequences to proteome dataset? What tools can be used to visualize peptide mapping result, like RNA-seq browsers?

Thank you very much!

peptide

• 3,660 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by biolab

1 answer

PIR peptide match

UCSC BLAT can produce a useful result for longer more unique peptides

Some mass-spec matching algorithms may also allow sequence-only inputs

• 0 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by cdsouthan

Thank you cdssouthan.

• 0 views • link

written 12.1 years ago by biolab

More posts like this

Kallisto bustools for scRNA-seq
written 3.4 years ago by t.ru •

Hi, I followed several tutorials about single cell rna-seq analysis for paired end. However, I need to quantify single ends scRNA-seq dataset. I have used …
Single cell RNASeq data with only R2.fastq
written 5.7 years ago by shenwei1376 •

Hi everyone, I downloaded some single cell RNA-Seq data from SRA sites. Unfortunately, only the R2.reads (~100bps) was uploaded for all the SRR files (SRR11573310...). …
How to embed genome browser in a web site?
written 9.3 years ago by biolab

Dear All, I am asking you for the ways of embedding genome browser on a web site, so as to visualize genome easily by others. …
Tophat vs Tophat-fusion concordant alignment rate
written 9.8 years ago by IP

Hi everyone! I am working with RNA-seq paired-end data. When I run tophat-fusion on a dataset, I get mapping percentage of 70-80% for both left …
how to test if BLAST installed in perl script?
written 11.6 years ago by biolab

Hi, eveyone, In a perl script, I want to test if blast was installed using the following lines. However on a computer without BLAST, there …
Perl script: generate pseudo-CDSs from intergenic region
written 11.7 years ago by biolab

Hi everyone Recently I read a paper (Genetica (2009) 137:159-164), in which the authors generate pseudo-CDSs (in other words, negative dataset) based on intergenic sequences. …
What tools to perform alignment without adding gaps in?
written 11.8 years ago by biolab

Hi everyone I have about one hundred short sequences (each 20 nt long), and need to perform sequence alignment. I found both CLUSTALX and MUSCLE …
How to draw mapping graph?
written 12.0 years ago by biolab

Hi everyone, I have mass spec peptide data. A simple example is shown below. ``` pep_sequence start end protein_id ACKJKAC 2 8 AT5G0030 ALLKDK 30 …
perl script:Needleman/Wunsch dynamic programming
written 12.1 years ago by biolab

Dear all, I read a reference, in which the authors used a perl script for Needleman-Wunsch dynamic programming algorithm. I am wondering does anyone could …
Tools For Mamalian Mirna Target Prediction
written 12.6 years ago by biolab

<p>Hi everyone,</p> <p>I am interested in mamalian miRNA target prediction. To my knowledge, the classical software for miRNA target prediction in mammales is <code>Targetscan</code>, which …