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tbl Format

The tbl format is used at the BMERC to describe dna and protein sequences. Its format in sed/perl notation is: 

[A-Z_a-z0-9]+\t[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]+\n$
[A-Z_a-z0-9]+\t[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]+\n$
...

In english the format is:
A sequence id followed by a tab then a sequence and ending with a newline.

Here is an example: 

5ADH    STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF

Yeast Cliques

A yeast clique is a group of related yeast genes which have been grouped by a common blast score, or some other heuristic into clusters. At present some yeast genes are in more than one cluster or clique, which may indicate a multi-domain protein. The information contained in these cliques has come primarily from the GeneQuiz Consortium and the Mips Genome Commission.

Raw Protein

A raw protein format is used at the BMERC to describe a single protein sequence. Its format in sed/perl notation is: 

^[ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy \t\n]+$

In english the format is:
A string with only the allowed 20 amino acid letters with optional whitespace (space, tab, and newline) characters included within it.

Here is an example: 

MVVFKNIGHIITKALALGSSTVMMGGMLAGTTESPGEYLYQDGKRLKAYRGMGSIDAMQKTGTKGNAST
SRYFSESDSVLVAQGVSGAVVDKGSIKKFIPYLYNGLQHSCQDIGCRSLTLLKENVQSGKVRFEFRTAS
AQLEGGVNNLHSYEKRLHN

Raw DNA

A raw dna format is used at the BMERC to describe a single dna sequence. Its format in sed/perl notation is: 

^[ACGTacgt \t\n]+$

In english the format is:
A string with only the allowed 4 dna letters with optional whitespace (space, tab, and newline) characters included within it.

Here is an example: 


ATGGCATCCACCGATTTCTCCAAGATTGAAACTTTGAAACAATTAAACGCTTCTTTGGCTGACAAGTCATACATTGAAG
GGTATGTTCCGATTTAGTTTACTTTATAGATCGTTGTTTTTCTTTCTTTTTTTTTTTTCCTATGGTTACATGTAAAGGG
AAGTTAACTAATAATGATTACTTTTTTTCGCTTATGTGAATGATGAATTTAATTCTTTGGTCCGTGTTTATGATGGGAA
GTAAGACCCCCGATATGAGTGACAAAAGAGATGTGGTTGACTATCACAGTATCTGACGATAGCACAGAGCAGAGTATCA
TTATTAGTTATCTGTTATTTTTTTTTCCTTTTTTGTTCAAAAAAAGAAAGACAGAGTCTAAAGATTGCATTACAAGAAA
AAAGTTCTCATTACTAACAAGCAAAATGTTTTGTTTCTCCTTTTAAAATAGTACTGCTGTTTCTCAAGCTGACGTCACT
GTCTTCAAGGCTTTCCAATCTGCTTACCCAGAATTCTCCAGATGGTTCAACCACATCGCTTCCAAGGCCGATGAATTCG
ACTCTTTCCCAGCTGCCTCTGCTGCCGCTGCCGAAGAAGAAGAAGATGACGATGTCGATTTATTCGGTTCCGACGATGA
AGAAGCTGACGCTGAAGCTGAAAAGTTGAAGGCTGAAAGAATTGCCGCATACAACGCTAAGAAGGCTGCTAAGCCAGCT
AAGCCAGCTGCTAAGTCCATTGTCACTCTAGATGTCAAGCCATGGGATGATGAAACCAATTTGGAAGAAATGGTTGCTA
ACGTCAAGGCCATCGAAATGGAAGGTTTGACCTGGGGTGCTCACCAATTTATCCCAATTGGTTTCGGTATCAAGAAGTT
GCAAATTAACTGTGTTGTCGAAGATGACAAGGTTTCCTTGGATGACTTGCAACAAAGCATTGAAGAAGACGAAGACCAC
GTCCAATCTACCGATATTGCTGCTATGCAAAAATTA

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James Freeman<jfreeman@darwin.bu.edu>

Last modified: Thu Mar 26 20:12:21 EST 1998