Hi Jimmy, Thanks for the tip. I found the blank line in the middle of all the sequences and this correction has worked.
Thanks! Adam On Friday, September 29, 2017 at 11:59:23 AM UTC-5, Jimmy Eng wrote: > > Adam, > > Try removing the first blank line in your fasta file and see if that fixes > the problem. > > On Fri, Sep 29, 2017 at 8:06 AM, Adam R <[email protected] <javascript:>> > wrote: > >> Woops. Yes this is my mistake when copying/pasting into the post. But the >> the fasta file attached is correct with >sp|uniprot|gene_human for all >> entries. >> >> Adam >> >> >> On Friday, September 29, 2017 at 9:04:09 AM UTC-5, Eric Deutsch wrote: >>> >>> Greater than symbol should be first on the line. Instead of: >>> >>> >>> >>> sp>|Q13547|HDAC1_HUMAN >>> >>> >>> >>> must be: >>> >>> >>> >>> >sp|Q13547|HDAC1_HUMAN >>> >>> >>> >>> Eric >>> >>> >>> >>> >>> >>> *From:* [email protected] [mailto: >>> [email protected]] *On Behalf Of *Adam R >>> *Sent:* Thursday, September 28, 2017 8:41 PM >>> *To:* spctools-discuss <[email protected]> >>> *Subject:* [spctools-discuss] "- Search progress: Error - database >>> file, expecting definition line here." Error with custom database >>> >>> >>> >>> Hi Everyone, >>> >>> I am trying to assemble a customized fasta database to search spectra >>> against. I believe I had the correct format as: >>> >>> sp>|Q13547|HDAC1_HUMAN Histone deacetylase 1 OS=Homo sapiens GN=HDAC1 >>> PE=1 SV=1 >>> >>> MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKAN >>> >>> AEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAS >>> >>> AVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHG >>> >>> DGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAI >>> >>> FKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGG >>> >>> GGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLE >>> >>> KIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEDDPDKRISICSSDKRIACEEEF >>> >>> SDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVK >>> >>> LA >>> >>> >>> >>> With all over the other proteins following the same format. I haven't >>> had issues with the past when copying and pasting in sequences from the GPM >>> crapome database >>> >>> so I am not sure what is wrong about it... >>> >>> Thanks, >>> >>> Adam >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at https://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
