Bmerc Logo

Who We Are

History and Mission
Personnel


Format Descriptions

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

BMERC main menu   Computational Biology   What's New   Web-Site Map


Sean Quinlan <wwwadmin@darwin.bu.edu>
last modified: Thursday, January 21, 1999 5:51:56 PM